>> For internal ancestral operations, it does, the names are needed to
>> know which files to access when, say, you request a diff operation.
>
> If I read the code correctly, then all we need to do is upload the second version of 'Monticello-bf.540' as 'Monticello-bf.540(1).mcz' to trunk. Then MC should find both files when looking up the ancestry, it should parse the actual version ID, and use the right one.

Yo!  You're right!!

      'Monticello-bf.540' asMCVersionName = 'Monticello-bf.540(1).mcz'
asMCVersionName   "true"

Oh my, what a rabbit-hole of a discussion we had if, all along, all we
had to do was rename the file!  I'm glad we ultimately identified the
fix (which was right in front of us all along, lol!) and even more
delighted that we'll be able to make our repositories whole in spite
of existing duplicates!

Thanks Bert and all!

 - Chris