Same thing happens when upgrading files. If I import my old files (FLAC), Plex creates a new album for them. Using your method works, but is the same annoyance as with the Plex Dance, since I have to move the files over by hand anytime I want to make a change.
I have also noticed the same issue when I convert from 24bit FLAC to 16bit.
I think scanning should work the same as it does for all other media, this just makes things confusing and tedious.
