Lois, the UNDO merge tool is rough. It was apparently a difficult problem to solve programmatically and it was a long time in test; a reason it's a "curator only / on request tool" is it's still not really "ready for prime time," and whatever residue (such as correct management) is handled manually. It also takes a while to run, which indicates it takes not trivial computing resources.
I can't say for sure but I find it difficult to believe this script - or indeed any other I know of - is capable of undoing the "big tree = yes" flag (however it is actually written!).
If a separate standalone tree is desired, the MyHeritage platform is available, and transparency / portability between the two structures only improves as time goes on.
Hope this helps.
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