This also happened in June. Uploading LOTW causes a duplicate QSO, I think because one QSO somewhere in my 74,549 QSOs has no data or Callsign and DXKeeper adds the next QSO and creates a dupe. I THINK!
FYI - all my QSOs are loaded in DXKeeper via N1MM Logger.
I've misplaced the complicated info you sent last time this happened.
73, Art W2NRA CWOPS #1955