Yes. I had this same problem a few weeks ago.

In an aircraft swap, it indeed re-seats many, even those people in seats that exist on the new seat map. I got booted out of the exit row aisle to a non-reclining window seat right before check in and someone else took my old seat at check in so I couldn't get it back, even though I picked up on it 30 minutes after it happened.

All I could do was complain and get some miles sent my way. GA was able to get me to non-reclining aisle after boarding.

Yet another instance of bad logic in their systems that has probably been there awhile.