I have a strange problem. I regularly download PDF files from different sources. In order to apply OCR, if absent or problematic, I usually change all the permissions of those files, but every time I do so, the file disappears and I can’t do anything to make it visible unless I reboot. This happens when I temporarily save the PDF to the Desktop only and change those permissions with the GUI. My installation has nothing weird or tweaked.
I’ve faced the same ―not that serious but annoying― problem for several weeks, if not months, both under X11 and Wayland (if that has something to do).
I seem to recall someone else complaining about this bug, and IIRC it was fixed in a recent 6.1 release - but I see that you are more or less current. Can you check what version of Dolphin do you use?
Note that this is a fresh Arch-based installation of 2-3. I already had the problem. I made a tiny video, but apparently I can’t share it here.
From “Owner: Can view & modify, Group: can only view and Others: can only view” to “Can view & modify” to all three of them (I reverted those last two changes and still the file is gone). Only when the PDF in on Desktop.
Updated to version 6.1.2 yesterday and Dolphin 24.05.2, but still the same problem. I shall reply again to this post only if I get rid of the problem in the future (let’s see if 6.1.3 is the one) or if someone needs anything else.
Finally, version 6.1.3 does not have that problem anymore (at least, I can not reproduce it). As @guss77 assumed earlier, the issue had been resolved, but we simply had to wait for the current version to become available.