You have to set the library.RootFolder.Properties["client_MOSS_MetadataNavigationSettings"] property to get change the per location view settings using the SharePoint Object Model.

   1: using (SPSite site = new SPSite("http://blre3r15-4"))
   2:             {
   3:                 //TaxonomySession session = new TaxonomySession(site);
   4:                 using (SPWeb web = site.OpenWeb())
   5:                 {
   6:                     SPList library = web.Lists["shared documents"];
   7:                     SPContentTypeCollection lsl = library.ContentTypes;
   8:                     foreach (SPContentType contenttype in lsl)
   9:                     {
  10:                         Console.WriteLine(contenttype.Id.ToString());
  11:                     }
  12:  
  13:                     foreach (SPView view in library.Views)
  14:                     {
  15:                         Console.WriteLine(view.ID.ToString());
  16:                     }
  17:                     System.Xml.XmlDocument document = new System.Xml.XmlDocument();
  18:                     //document.Load("c:\\cases\\Settings.xml");
  19:                     document.LoadXml(library.RootFolder.Properties["client_MOSS_MetadataNavigationSettings"].ToString());
  20:                     System.IO.StreamWriter writer = new System.IO.StreamWriter("c:\\cases\\Settings.xml");
  21:                     writer.Write(library.RootFolder.Properties["client_MOSS_MetadataNavigationSettings"].ToString());
  22:                     writer.Close();
  23:                     //library.RootFolder.Properties["client_MOSS_MetadataNavigationSettings"] = document.OuterXml.ToString();
  24:                     //library.RootFolder.Update();
  25:                     //library.Update();
  26:                     //web.Update();
  27:                     Console.WriteLine(library.RootFolder.Properties["client_MOSS_MetadataNavigationSettings"].ToString());
  28:                     SPViewCollection collection = library.Views;
  29:                     
  30:                     //MetadataNavigationSettings mdnSettings = MetadataNavigationSettings.GetMetadataNavigationSettings(library);
  31:                     //mdnSettings.SettingsXml = document.OuterXml.ToString();
  32:                     //MetadataNavigationSettings.SetMetadataNavigationSettings(library, mdnSettings);
  33:                     //Console.WriteLine(mdnSettings.SettingsXml.ToString());
  34:                     Console.ReadKey();
  35:                                         
  36:                 }
  37:             }
   1: <MetadataNavigationSettings SchemaVersion="1" IsEnabled="True" AutoIndex="True"><NavigationHierarchies><FolderHierarchy HideFoldersNode="False" />
   2: <MetadataField FieldID="03e45e84-1992-4d42-9116-26f756012634" FieldType="ContentTypeId" CachedName="ContentTypeId" CachedDisplayName="Content Type">
   3:   <ViewSettings UniqueNodeId="0x01010070FC6B859DF4CD4FAEDD269B75BE2C8E003443C1064EC2D9489B7D978018AFFEF3">
   4:     <View ViewId="b0e7c6b8-7a05-4943-8323-bc7d1ab90c4a" CachedName="Test2" Index="2" CachedUrl="Shared Documents/Forms/Test2.aspx" />
   5:     <View ViewId="2017c43f-7b0d-4580-9d9d-d3c699b51b6a" CachedName="All Documents" Index="1" CachedUrl="Shared Documents/Forms/AllItems.aspx" />
   6:     <View ViewId="82185a44-dd31-4a12-91bf-da6798ff2c26" CachedName="Test1" Index="0" CachedUrl="Shared Documents/Forms/Test1.aspx" />
   7:     <View ViewId="c1bd6b7b-ba53-4b0f-984d-3c24886dd4f5" CachedName="Merge Documents" Index="-1" CachedUrl="Shared Documents/Forms/Combine.aspx" />
   8:     <View ViewId="403a91bb-2f07-4eef-bcaa-f14778148edd" CachedName="Relink Documents" Index="-2" CachedUrl="Shared Documents/Forms/repair.aspx" />
   9:     <View ViewId="79b33591-e594-4d4d-afd0-fd700a08f480" CachedName="assetLibTemp" Index="-3" CachedUrl="Shared Documents/Forms/Thumbnails.aspx" />
  10:     <View ViewId="d38fef41-7cf5-4a73-adc9-7edb956addfc" CachedName="" Index="-4" CachedUrl="SitePages/Home.aspx" />
  11:   </ViewSettings><ViewSettings UniqueNodeId="0x01010090C01EC2217EB24E9C25C0B20DA04FE0"><View ViewId="82185a44-dd31-4a12-91bf-da6798ff2c26" CachedName="Test1" Index="0" CachedUrl="Shared Documents/Forms/Test1.aspx" /><View ViewId="2017c43f-7b0d-4580-9d9d-d3c699b51b6a" CachedName="All Documents" Index="1" CachedUrl="Shared Documents/Forms/AllItems.aspx" /><View ViewId="b0e7c6b8-7a05-4943-8323-bc7d1ab90c4a" CachedName="Test2" Index="2" CachedUrl="Shared Documents/Forms/Test2.aspx" /><View ViewId="c1bd6b7b-ba53-4b0f-984d-3c24886dd4f5" CachedName="Merge Documents" Index="-1" CachedUrl="Shared Documents/Forms/Combine.aspx" /><View ViewId="403a91bb-2f07-4eef-bcaa-f14778148edd" CachedName="Relink Documents" Index="-2" CachedUrl="Shared Documents/Forms/repair.aspx" /><View ViewId="79b33591-e594-4d4d-afd0-fd700a08f480" CachedName="assetLibTemp" Index="-3" CachedUrl="Shared Documents/Forms/Thumbnails.aspx" /><View ViewId="d38fef41-7cf5-4a73-adc9-7edb956addfc" CachedName="" Index="-4" CachedUrl="SitePages/Home.aspx" /></ViewSettings></MetadataField></NavigationHierarchies><KeyFilters /><ManagedIndices><ManagedIndex IndexID="03e45e84-1992-4d42-9116-26f756012634" IndexFieldName="ContentTypeId" IndexFieldID="03e45e84-1992-4d42-9116-26f756012634" /></ManagedIndices><ViewSettings UniqueNodeId=""><View ViewId="2017c43f-7b0d-4580-9d9d-d3c699b51b6a" CachedName="All Documents" Index="0" CachedUrl="Shared Documents/Forms/AllItems.aspx" /><View ViewId="82185a44-dd31-4a12-91bf-da6798ff2c26" CachedName="Test1" Index="4" CachedUrl="Shared Documents/Forms/Test1.aspx" /><View ViewId="b0e7c6b8-7a05-4943-8323-bc7d1ab90c4a" CachedName="Test2" Index="5" CachedUrl="Shared Documents/Forms/Test2.aspx" /></ViewSettings></MetadataNavigationSettings>
   1: using System;
   2: using System.Collections.Generic;
   3: using System.ComponentModel;
   4: using System.Data;
   5: using System.Drawing;
   6: using System.Linq;
   7: using System.Text;
   8: using System.Windows.Forms;
   9: using Microsoft.SharePoint;
  10: using Microsoft.Office.Server;
  11: using Microsoft.Office.DocumentManagement.MetadataNavigation;
  12: using System.Xml;
  13:  
  14: namespace MetaDataViewAssosiaction
  15: {
  16:     public partial class Form1 : Form
  17:     {
  18:  
  19:        private const string DefaultListSettingsXmlString =  @"<MetadataNavigationSettings SchemaVersion=""1"" IsEnabled=""true"" AutoIndex=""True""><NavigationHierarchies><FolderHierarchy /></NavigationHierarchies><KeyFilters></KeyFilters></MetadataNavigationSettings>";
  20:  
  21:         
  22:         public Form1()
  23:         {
  24:             InitializeComponent();
  25:         }
  26:         SPSite site;
  27:         private void btnFillData_Click(object sender, EventArgs e)
  28:         {
  29:             string siteURL = textBox1.Text.ToString().Trim();
  30:             site = new SPSite(siteURL);
  31:             FillWebs(site);
  32:            
  33:         }
  34:  
  35:         private void FillWebs(SPSite site)
  36:         {
  37:             foreach (SPWeb web in site.AllWebs)
  38:             {
  39:                 lstWeb.Items.Add(web.Name);
  40:             }
  41:         }
  42:  
  43:         private void FillList()
  44:         {
  45:             using (SPWeb web = site.OpenWeb(this.lstWeb.SelectedItem.ToString()))
  46:             { 
  47:                 foreach(SPList List in web.Lists)
  48:                 {
  49:                     lstList.Items.Add(List.Title);
  50:                 }
  51:                 
  52:             }
  53:  
  54:         }
  55:  
  56:         DataTable table = null;
  57:         private void FillContentTypes()
  58:         {
  59:             table = new DataTable();
  60:             DataColumn IDColumn = new DataColumn("ID");
  61:             IDColumn.DataType = typeof(string);
  62:             table.Columns.Add(IDColumn);
  63:             
  64:             DataColumn NameColumn = new DataColumn("ContentTypeName");
  65:             NameColumn.DataType = typeof(string);
  66:             table.Columns.Add(NameColumn);
  67:             using (SPWeb web = site.OpenWeb(this.lstWeb.SelectedItem.ToString()))
  68:             {
  69:  
  70:                 SPList list = web.Lists[this.lstList.SelectedItem.ToString()];
  71:                 foreach (SPContentType ContentType in list.ContentTypes )
  72:                 {
  73:                     DataRow row = table.NewRow();
  74:                     row["ID"] = ContentType.Id;
  75:                     row["ContentTypeName"] = ContentType.Name;
  76:                     table.Rows.Add(row);
  77:                     
  78:                 }
  79:  
  80:             }
  81:  
  82:             lstContentTypes.DataSource = table;
  83:             lstContentTypes.DisplayMember = table.Columns["ContentTypeName"].ColumnName;
  84:             lstContentTypes.ValueMember = table.Columns["ID"].ColumnName;
  85:             
  86:         }
  87:  
  88:         DataTable ViewTable = null;
  89:         private void FillViews()
  90:         {
  91:             ViewTable = new DataTable();
  92:             DataColumn IDColumn = new DataColumn("ID");
  93:             IDColumn.DataType = typeof(string);
  94:             ViewTable.Columns.Add(IDColumn);
  95:  
  96:             DataColumn NameColumn = new DataColumn("ViewName");
  97:             NameColumn.DataType = typeof(string);
  98:             ViewTable.Columns.Add(NameColumn);
  99:             using (SPWeb web = site.OpenWeb(this.lstWeb.SelectedItem.ToString()))
 100:             {
 101:                 SPList list = web.Lists[this.lstList.SelectedItem.ToString()];
 102:                 foreach (SPView  View in list.Views)
 103:                 {
 104:                     DataRow row = ViewTable.NewRow();
 105:                     row["ID"] = View.ID;
 106:                     row["ViewName"] = View.Title;
 107:                     ViewTable.Rows.Add(row);
 108:                 }
 109:  
 110:             }
 111:  
 112:             lstViews.DataSource = ViewTable;
 113:             lstViews.DisplayMember = ViewTable.Columns["ViewName"].ColumnName;
 114:             lstViews.ValueMember = ViewTable.Columns["ID"].ColumnName;
 115:         }
 116:  
 117:         private void lstWeb_SelectedIndexChanged(object sender, EventArgs e)
 118:         {
 119:             FillList();
 120:         }
 121:  
 122:         private void lstList_SelectedIndexChanged(object sender, EventArgs e)
 123:         {
 124:             FillContentTypes();
 125:             FillViews();
 126:             MessageBox.Show("Done");
 127:  
 128:         }
 129:  
 130:         private void button1_Click(object sender, EventArgs e)
 131:         {
 132:             string XML = GenerateXML();
 133:             MessageBox.Show(XML);
 134:         }
 135:  
 136:         string XmlElementNameRootElement = "MetadataNavigationSettings";
 137:         string XmlAttributeNameSchemaVersion = "SchemaVersion";
 138:         string XmlAttributeNameIsEnabled = "IsEnabled";
 139:         string XmlAttributeNameAutomaticIndexManagement = "AutoIndex";
 140:         string XmlElementNameNavigationHierarchies = "NavigationHierarchies";
 141:         string XmlElementNameKeyFilters = "KeyFilters";
 142:         string XmlElementNameFolderHierarchy = "FolderHierarchy";
 143:         private string  GenerateXML()
 144:         {
 145:             StringBuilder sb = new StringBuilder();
 146:  
 147:             XmlWriterSettings writerSettings = new XmlWriterSettings();
 148:             writerSettings.OmitXmlDeclaration = true;
 149:             writerSettings.Indent = false;
 150:             writerSettings.NewLineHandling = NewLineHandling.None;
 151:  
 152:             XmlWriter writer = XmlWriter.Create(sb, writerSettings);
 153:  
 154:             writer.WriteStartElement(XmlElementNameRootElement);
 155:             writer.WriteAttributeString(XmlAttributeNameSchemaVersion, "1");
 156:             writer.WriteAttributeString(XmlAttributeNameIsEnabled, "True");
 157:             writer.WriteAttributeString(XmlAttributeNameAutomaticIndexManagement, "True");
 158:             // Should we add the cached list Url and ID
 159:  
 160:             //// Serialize Navigation hierarchies collection
 161:             writer.WriteStartElement(XmlElementNameNavigationHierarchies);
 162:             writer.WriteStartElement(XmlElementNameFolderHierarchy);
 163:             WriteStorageXml(writer);
 164:             writer.WriteEndElement();
 165:             writer.WriteEndElement(); // XmlElementNameNavHierarchies
 166:  
 167:             writer.WriteStartElement(XmlElementNameKeyFilters);
 168:             //MetadataNavigationSettings.WriteStorageXml<MetadataNavigationKeyFilter>(this.ConfiguredKeyFilters, writer);
 169:             writer.WriteEndElement(); // XmlElementNameKeyFilters
 170:  
 171:  
 172:             writer.WriteEndElement(); // XmlElementNameRootElement
 173:  
 174:             writer.Flush();
 175:             writer.Close();
 176:  
 177:             return sb.ToString();
 178:           
 179:         }
 180:  
 181:         string xmlElementNameViewSettings = "ViewSettings";
 182:         string XmlAttributeNameUniqueNodeId = "UniqueNodeId";
 183:         private void WriteStorageXml(XmlWriter writer)
 184:         {
 185:            
 186:             writer.WriteStartElement(xmlElementNameViewSettings);
 187:             writer.WriteAttributeString(XmlAttributeNameUniqueNodeId, "");
 188:             writer.WriteEndElement();
 189:         }
 190:  
 191:         private void btnMap_Click(object sender, EventArgs e)
 192:         {
 193:             DataRowView row = (DataRowView)this.lstContentTypes.SelectedItem;
 194:             DataRowView viewRow = (DataRowView)this.lstViews.SelectedItem;
 195:             string strMapping = row.Row["ContentTypeName"].ToString() + ";" +
 196:                                 this.lstContentTypes.SelectedValue.ToString() + ";" +
 197:                                 viewRow.Row["ViewName"].ToString() + ";" +
 198:                                 this.lstViews.SelectedValue.ToString();
 199:             
 200:             this.lstMapping.Items.Add(strMapping);
 201:         }
 202:     }
 203: }