Solved. Had to run flatpak remove --all
followed by flatpak repair
to prune caches, then re-install every app again. But configs and logins seem to remain intact.
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Thanks for posting the solution!
If you happen to be using a BTRFS or XFS file system, you might want to try duperemove. It will help you reclaim usable disk space without deleting any files, by using those filesystems' built-in support for data deduplication and copy-on-write. In other words, it will make duplicate files point to the same data on disk, but still work as individual files. Files will appear and function exactly the same, and editing one copy will not change another (unlike with hard links, for example). That way it won't interfere with cases like Flatpak or Python virtual environments where you really need multiple copies of the same files.