Um, there should not be two sent folders, that's my first thought.
Exchange servers have a notion of what "the" sent folder is, and AquaMail works with that one.
Second, letting them sync "as incoming" is strange too -- it means that Aqua won't know them as "folders for sent messages".
There is got to be a third one, the predefined Exchange server side Sent folder.
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Or putting it differently:
Exchange has a predefined Sent folder (actual name may vary), and that's the one AquaMail is going to try and use.
Seems like your account's folder configuration wrt. sent folders is different, messed up.