I would only export to GEDCOM if I were transferring the information to another software program. GEDCOM doesn't support everything FTM does and vice versa. You're bound to lose stuff by using GEDCOM.
Your same concept will work, however, by exporting to separate FTM trees. Here's what I would do.
1) Create a new blank tree called "combined.ftm"
2) Take my first tree (e.g. "tree-a") and export people from it that I know are not duplicated in any of the other trees. I would call this "uniques-from-tree-a.ftm". I would then export everyone else from tree-a to a new file called "manual-merges-from-tree-a.ftm". I would then tuck tree-a away in a safe place.
3) I would then open up combined.ftm and import uniques-from-tree-a.ftm.
4) I would then repeat two steps above for all the other trees, merging the known non-duplicates each time with the combined.ftm. When you're done with this, you should have one tree left over to be merged from each of the originals:
5) I would then merge each of the leftover trees, manually deciding on each person. (I wouldn't let FTM make any decisions.) I would also check each merged duplicate against the original to make sure all the facts came over.