Two things I can think of to check:
1. In Dolphin's General settings, you can change the directory of where it is looking for the memory cards. If the Flatpack version saved them somewhere else, you can move them to the location Dolphin is looking for them?
2. If the save files are already in the correct directory, check the owner of the files by running "sudo ls -l" in the terminal in the directory. If it's not your user/group, chown the files to your user?
1. In Dolphin's General settings, you can change the directory of where it is looking for the memory cards. If the Flatpack version saved them somewhere else, you can move them to the location Dolphin is looking for them?
2. If the save files are already in the correct directory, check the owner of the files by running "sudo ls -l" in the terminal in the directory. If it's not your user/group, chown the files to your user?