I updated Dolphin on my system and now my games can't acces saved data

[OuterSpace]

I am using Ubuntu 20.04 and I was using Dolphin from a Flatpak (Dolphin 5.0-12716). I uninstalled it and installed Dolphin from the main repository and now the games can't access the saved data. I've been checking the folders and the GCI files are still there, but they won't load into the game. I tried reinstalling the flatpak version but it still doesn't load the data and I can't find the same version I uninstalled. The games just always just asks me to create a new save file.