OK but why does the process of cloning the drive result in good aliases going bad? The path of the file hasn't changed.
It's as if the alias is referring to the file by some kind of id, rather than its path, and this id can change as part of the cloning process, resulting in the alias referring to a completely different file on the cloned drive that happens to have the same id.
Could it be, for example, that the aliases are using hard links (as apparently
used by Time Machine) and the inodes of the files (sometimes?) change in the backup, or something weird like that?