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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.

Now, if you were to add another folder there

... you would be interfering with things  that app wants to handle. depending on where exactly you place new files. For one you have to have admin writing privileges there, because program files is a protected folder.  I suspect this is the reason that itch miuses that other folder. It is a user folder.

If you place files into the cache dicrectory of steam, i do not know how it would handle it and do not  want to find out. if you use the installation directory  of a game, i do know that your modifications are safe. with uninstall, added files and folders are kept.

now if you placed your own downloads into a folder that is considered temp by the app and itch app does not keep track of downloads and occasionaly cleans out everything there because it does not keep a manifest ... that might be what has happened. 

you should use a link to your download stash and not put your download stash inside a hidden data subfolder that is managed by an app that has nothing to do with your downloads.