Instead of using the Merge tool, what if one did this:
Export all of the family files as GEDCOM files, create a new family tree in FTM (without adding any people) and then import all those individual GEDCOM files into that new family tree.
Would that solve the problem of having duplicate people when using the 'Merge' tool? Or would this create a whole new set of issues?
(I've never imported a GEDCOM file so I honestly don't know.)