Recently, we published a KB article that is related to files being downloaded from version control with the incorrect contents.  The symptoms from the article:

After restoring a Team Project Collection (TPC) from a backup, files downloaded from Team Foundation Server through version control operations may have incorrect contents.

An example of this is that you perform a Get operation, which downloads a file named Foo.cs, but the contents of Foo.cs are actually from the file Bar.cs.  This mismatched content is NOT the result of corruption in the database – it is an issue with stale cache contents.  From the article:

In the event of a TPC restore, it is possible that files added since the last backup was taken will be cached on the AT with a FileID that was assigned between the time backup was taken and the restore was applied.  If the version control cache was not purged prior to the TPC restore, FileIDs that were reassigned to new files may result in false positive cache-hits, leading to the download of incorrect file contents.

We found this issue very late in the 2010 cycle, and we plan to revisit this in the first service pack.  If you believe you have hit this issue, visit the KB article for details on how to correct the problem.  Also, if you’re seeing file corruption that is not related to this, please let me know as this would be an issue we would want to investigate and fix ASAP.

KB Article 2025763: http://support.microsoft.com/default.aspx?scid=kb;en-US;2025763