Which system, 3DS or Switch?
If it's the Switch, am I right to guess that your Pokemon received by trade is done on OFW, and checkpoint dumping is done via CFW?
If your situation is indeed as I described, your OFW and CFW profiles have unlinked. It is not known how they unlinked, but I can only imagine you've done some kind of update (maybe game, firmware etc) that caused them to unlink. Thus, your CFW and OFW saves are different now.
If the above isn't your described issue, ignore the paragraph, and report to us all the details.
(Device? using CFW? Using emunand? etc)