That's because technically you uninstalled only one game, with all the data in game folder.. Information about all the rest of your games still persist in registry.
This wouldn't happen if you use scan and import folders instead of import folder..

Thanks for the info and looking into this, I appreciate it.

Turns out I have an Undelete program and I used it to scan my drive and undelete my files so I got my games back. Still I think I'm going to do clean installs right now and simply transfer my save games over, don't think I want to import anymore.

Glad you got your games back : )
This could happen to anyone. I used to mess up with Galaxy a lot, but never before tried importing main games directory this way.. It's still work in progress, probably went to open beta a bit too early and some things need to be improved to avoid problems like that in the future. Sorry for any inconvenience.

edit:
I can assure you you're completely safe with scan and import folders. You get there by clicking plus sign on the top-left of the Galaxy window. This way Galaxy scans all the folders in directory you pointed for .info files. If gets one, adding the game to Galaxy and comparing with server data, if some files doesn't match then downloads them.
On the other hand, if you'd read pop-up warning carefully this wouldn't happen for sure..

I read about a case like yours a while back. I went and immediately uninstalled GOG galaxy. I'll stick with the downloader for now.