Upgraded to 3.1 on server and apps in builder gone

[SteveClark]

I upgraded one of our older servers to 3_1_x64. It installed fine over the older version but when I went back into Builder, all of the apps were gone. I expected, as other upgrades I had done, to see the Upgrade button next to each app but I don't even get the list of apps. I know they are there in the folder and the url still works. I cleared cache but still no listing. What went wrong in the upgrade and how can I get my apps back into Builder?

[SteveClark]

Let me ask a simpler question. What are the files in the apps that the Upgrade button upgrades? I compared the files and folders from a new 3.1 app to one of the old app and while I can copy over the pertinent files (like Map and Behaviors), I think I may miss something. Copy over the whole folder will overwrite the new dll and xap, so I should upgrade only what I need to. The reason the file list in the Builder is gone is because the Sites folder got overwritten, which I don't think it should have done.