Guys first of all we're really sorry for this problem, it shouldn't have happened. We're treating it as high priority and currently investigating. Do you have any 100% reproduction to the problem? Which installer were you using (there's a version in the filename)?

In the meantime please avoid reinstalling the client to a different location, there's a know bug with it (Essential components missing) and do not install anything to the same folder as the client.

All currently known issues with the Client can be found in this post.

I've just checked it with Ultima V, purposely selecting parent folder (C:\Games) instead of the game (C:\Games\Ultima 5). After uninstalling the game other subfolders in C:\Games remained intact.

The only way to achieve such unfortunate result of parent folder being wiped, would be to select the checkbox to "Also remove my savegames and any user data" during the uninstallation, which would indeed wipe all the contents of the folder (and as the folder was mistakenly selected in the first place, this would really wipe it).

Until import option cannot magically guess that the selected folder was wrong, sadly there is no magical solution here and we will likely remove that checkbox for manually imported games as there is always a risk of selecting a wrong folder.
This is an unrelated issue to cimerians post, and to my knowledge it was fixed in 1.0.7 beta if not in 1.0.5.

The whole point of manual importing option was to allow users to import their installations coming from old installers, that did not include galaxy manifest files.

Initially we only had option to import games coming from newer installers ("Scan and import folders" available under "+" dropdown in sidebar) which worked similarly to what you suggest and was very user friendly and foolproof, but we had a lot of complains from users who said they don't want to redownload game installers...