Sometimes they get changed for a silly reason (someone just didn't think of the consequences). Sometimes they get changed because they have to - if I remember correctly it was Asterisk that needed to drop some copyrighted music samples and retagged old versions.

That shouldn't matter, then; it should just result in a new release.

You can't distribute the old versions with copyright violation. The problem doesn't go away just because you released a new version.

But then you have two different things (with and without copyrighted data) both with the same version. Wouldn't it be better to just remove the bad release, and publish a new one? They are, after all, not the same things, and shouldn't have the same release.

Good point, that would make sense. But same difference. Why is that not how it works?