On a just about up to date Ubuntu 24.04.2 LTS (kernel at 6.8.0-63.66, otherwise all good), VLC ran through my home directory systematically moving everything from symlinked directories on other partitions to the home directory. This was unexpected, and rather annoying, and it only stopped when it had filled up the home drive. VLC is a snap, version 3.0.20-1-g2617de71b6, which seems to be up to date.
I had opened VLC probably for the first time on this box, and converted a CD track. (Used a different app to to this afterwards)
Lots of log messages in /var/log/syslog said eg (where /home/myuser/Documents is the symlink to another partition):
@bud13wxqz
I had the same version as you and the vlc did not behave as yours has.
I had removed all snap infrastructure and used the .deb version of vlc.
I had that experience myself (files moved without being asked), had to restore from backup. This was and still is a reason for me to avoid using snaps as much as possible.
Are these partitions mounted under /media or /mnt ?
These are the only locations a confined snap like vlc can access outside of your home via the removable-media interface…
A normal cross partition symlink to any other location would just result in a permission denied error from the kernel.
This was a bug that has long been fixed since (well, the helper scripts are simply not used by the various toolkit extensions anymore), the problem here is that the vlc snap packaging has not been changed since 2019 or so (which is usually fine, the snaps re-build automatically when a new upstream release comes out, but in this case it simply means the bug persists until someone bumps the base: of the package to something newer than core18)
Note that vlc is also special here, usually the removable-media interface is not automatically connected, some media players got an exception on request (vlc among them) simply because playing media from USB is a typical use-case for them.
You could have manually disconnected it though to prevent any access to /media or /mnt mounted devices.