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@Dark_Arc @bl4kers
I can understand the confusion. But it kinda makes sense.... if my hypothesis is correct.
Proton Drive has the concepts of "My Files" and "Computers". Files stored under "Computer" (where you can have synced files for up to 10 computers, according to docs) tracks the files for each computer individually.
So when you uninstall Drive and delete the files, they are only stored in the cloud. But after reinstalling it again, it sees the files locally for that computer is gone ... so it gets removed in the cloud.
Had these files been moved to "My Files" in before the reinstall, this should not have happened.
At least, that's my theory.
Still, I would expect a sync program to ask "hey, do you want these files restored, to merge the local state, or replace the remote state?" before doing anything else.