For some reason I can't find the knossos config folder anymore, it doesn't seem to be at ~/.knossos on my Macs now. I blew away the data folder, which did remove its knowledge of my mods, but it did not re-run the first launch wizard to find FSO. Ok, I did manage to find that under Settings -> Install Retail or whatever it was called. But given that I ran it manually, the dialog did not make much sense as it said I was trying to install a mod that required FS2 retail data (I was just trying to install FS2 retail data though so that text is confusing I think). Also, after selecting the folder to copy the data from and hitting continue, the dialog closed but nothing else happened. No "copy complete", etc, and the button didn't disappear until I reloaded the settings page after checking the Home page to see Retail FS2 had indeed appeared. So, everything worked well enough, but the process was a little confusing. And where _is_ that config folder/file now if I want to reset this thing completely? I could have sworn I'd found it once before but it seems like it moved on me.
Also should mention, the reason I blew away the data directory is that the SCP mod had been installed in a broken state while SSL was broken, and after updating Knossos and checking file integrity, it did download files, but the mod metadata still seemed messed up, the images in both Home and Explore were still broken. Blowing away the data directory and starting it over seemed to be the only way to fix it. Probably a really edge case thing, but I thought you might want to know that the file integrity check didn't seem to 100% fix a broken mod install at the moment.