It’s repeatable here with a quicksave I have been working on since before upgrading (no custom units, just stock, Ch1/2 linked, with Ch3 used for a simple clock function). I can load it (works fine) then save into an empty slot… and when I reload it, Ch3’s units end up in Ch1-2.
If I look carefully at the messages during loading, it seems like the ‘correct’ Ch1-2 chain is loading, then these are replaced by the Channel 3 units.
Tried editing the original quicksave to clear channel 3, saving again to a new slot. But loading that version just gives the result that Ch1/2 is cleared following its chain being loaded.
Let me know if a copy of any of the quicksave files would help!