I'd be surprised if there's even one replay that gets broken as a result of changing it. Off the top of my head, I can think of a total of four levels that actually require the nuke in the solution (one of which isn't V1.47n-friendly for other reasons anyway); there's probably two or three more out there that I don't know of. Some of these don't even give you any skills, or would have no reason to use a skill at around the same time as the nuke. When using the nuke in a replay that doesn't actually require nuking (as a means of ending the replay), it's usually long after the last skill has been assigned.
Consistency is the main goal here, indeed.