You really want to avoid the downloader if at all possible. It does not behave with a great deal of antivirus and antispyware software. For some reason Adobe just doesn't get along with certain programs.
I would try, if you must use the downloader, deactivating your AV while you redownload everything individually. Also, before you do that, delete all traces of the game currently on your system. At this point, you may have to rename the main file again, but I'm willing to bet it's not corrupted.
The alternative method is to download each bit through your browser, but again you may need to disable your AV software to get the game to a non-corrupted state.
Hope this helps, and welcome to GOG, Grimgak :)