It never work. I've always done flatpak remove --unused every once in a while. At one time I checked my root filesystem using gnome's disk analyzer to see what takes the most space, that is when I found out /var/lib/flatpak/repo/ ate 80 gb of my disk.

As per several suggestion from github issues & forums, I did sudo flatpak repair and finally it did clean them up down to around 40-50. Several months later I kind of gone mad and delete everything in the repo directory. I noticed my apps still works. Until few days later when I wanted to update, Flatpak complained and redownload most of the deleted stuff 🤣

But after redownloading, it only took around 20 gb now, and after that Flatpak also pinned every package lmao so I have to unpin unimportant stuff any case they can be deleted using flatpak remove --unused

and I seem to be not the only one, like this person has their Flatpak directories almost 100 gb https://forums.linuxmint.com/viewtopic.php?t=435450

I realize I may also just remove all latex stuff, I was only using it to graduate. I'd just typst now for smaller things.