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Synchronized Favorites are a great feature and I have over 1400 synced between three computers.  Like the article listed above say "Sync has been disabled temporarily to prevent any further issues".  The unfortunate side-effect for most people (including me!) was the removal of some or all of your existing shortcuts from the local computer.  I have to admit I panicked when I noticed they were missing.  The good news is your Favorites are still available on your SkyDrive share in your Favorites folder.  Here are some steps you can use to "reload" the shortcuts on your computer manually until the sync is fixed.

1. Visit http://skydrive.live.com and click On the Favorites folder.
2. Click the "Download as a .zip file " link on the SkyDrive menu and save the file (Favorites.zip) in a local folder.
3. Open Windows Explorer and navigate to C:\Users\your-name-here\Favorites.
4. If there is anything left in the folder move it to another location for safe-keeping.  The Favorites folder should be empty now.
5. Open/Extract the Favorites.zip file from step 2 and place the contents into the Favorites folder in step 3 above.  

The procedure above should restore all you Favorites to the Favorites menu in IE.  Now we need to solve one more problem.  If you had shortcuts stored on your Links bar in the browser they may still be missing.  For whatever reason the "Links" folder (which corresponds to the Links menu bar inside the browser has been renamed to "Favorites Bar"  Look inside your Favorites folder from step 3 above.  If you have two "Favorites Bar" folders look inside each one.  If one is empty and the other has content rename the one with content "Favorites Bar - old".  Copy the contents of "Favorites Bar -old" to the "Favorites Bar" folder, restart the browser and your shortcuts on the menu bar within IE should be there.

Hope this helps.