Here is how I got all of my projects to repopulate.
Stop the service "DTools LANSync v5 Server".
The document that explains how to move the server states not to copy the "clientconfiguration.xml or DToolsCache.xml" files, however I copied them over and edited all references from the previous server name to the new server name.
Also everything that was in "D-Tools SI5 Projects" folder within the "My Documents" folder was copied over to the new server and I edited "FileMgrCache.xml" like I did with the other .xml files.
Restart the service "DTools LANSync v5 Server".
The files will then take a couple minutes to resync (this may take longer for your company depending on how many projects are in the folders).
After logging into SI5 I had to highlight each project and have it "Get latest version of all files for this project".
Seems to be working.
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