I don't know when the behaviour of pacman changed, maybe with one of the last updates. I moved some big programs to another partition and used a symlink which is pointing to the new location. This works fine the last years. But know I'm recognised that pacman, if it upgrades these program, it deletes all symlinks on the path to this program, and it creates new directories instead. This can crash the system in the worst case.

I don't know if symlinks are a bad practice, now i'm using mounts instead of symlinks, but the user should at least get a warning and pacman should cancel with an error.

Steps to reproduce:
# move a directory, like /opt/java to new place X
# create a symlink /opt/java to X
# pacman -S jre

Thank you,
Berger