Please read my reply to the post aboove yours. The issue seems not to be that my progress is wiped with any games, but rather that the installation folder. To explain further, let's use steam as a great example here since you mentioned it...
You install a game through steam, that game has a location inside steams installation location, where you can find all of the games you downloaded through Steam. This location is usually something like C:\Program Files (x86)\Steam\steamapps\common
Now, if you were to add another folder there, in other words, use the same folder for a game you download through a third party. What will happen when Steam updates, will it automatically force you to re-download all of your installed games you have on steam? No. Will it touch any of the additional folder you have added there? No.
I hope I make more sense now, and I apologize for the confusion since I am not really sure what the hell has happened myself, all I know is that all of my game is gone and that I need to re-install them. I don't mind doing that with the games I can download through Itch app itself, since it saves your progress in %appdata% anyway. But the games that I downloaded through third-party websites are also gone. And I honestly have no idea which games those were at this point.