@justdanyul There are some potential causes of this behavior. Electron apparently has some questionable ways of handling trash across different desktops. I don’t believe it’s a flatpak issue per se, more like the concept of “system trash” isn’t well-defined on Linux and projects like Electron have to hack their own implementations around it, which then might not even behave as expected when run in an environment that has strict permissions checks like in the case of flatpak.
This particular bug can at least be worked around – set Deleted files to Move to Obsidian trash (.trash folder) like so:
The Obsidian devs may eventually add a global option for default trash behavior, but in the meantime I’ve written a workaround that runs every time Obsidian launches.
All you need to do to update and restart Obsidian:
$ flatpak update md.obsidian.Obsidian --assumeyes
$ flatpak run md.obsidian.Obsidian
I hope that helps!