... of newly created and edited groups, dumping them all at the bottom of the list.
This is intended behaviour.
It is intended to keep new entries but lose their order???
Yes, I think that's the most expected way of handling this situation.
OK, though FTR, I think it is more expected to keep both or keep none.
But actually what I'd prefer is an Apply button to apply all changes, and then Cancel could be changed to the standard behaviour of discarding all (unApplied) changes.