I apologize, I understand that it's not so easy to understand my problem because I dont really know how to explain it.
So since some of the games I download for various reasons use external download links which you have to download through your browswer (in other words - not related to itch itself in any way) I wanted these games stored in the same location as the games that I DO download using the Itch app. So I created a new folder inside the itch app is located... This folder is where I directed all of my downloads, both from itch, and the external downloads.
When Itch updated somehow I now seem to have two versions of Itch on my computer, one is 25.5.1 and the other is 25.62. During the update it seemed that it caused this folder I created inside my itch app's installation location (of version 25.5.1) to simply vanish, along with the games there. I have now created a new folder in my 25.62 version as a location for games but I have to re-download them, and the ones I had downloaded manually through third parties are gone. I can't make sense of why this folder would be deleted, or even why I have a 25.5.1 folder still located on my computer at all post-update.
I hope I made more sense explaining my issue with this post.