Had this same issue with JKSV/Checkpoint, and can confirm that opening and exporting with pkhex works like a charm.I found a workaround, for whatever reason if I import and export the file in pkhex (even without modifications), I can restore on switch 2. If anyone is interested I can try checkpoint too
I needed to update Checkpoint to 3.8.0, and launch in full ram mode (Hold R and launch a regular game from switch home menu , then it will redirect to hbmenu) Then Checkpoint will launch without crashing.Unfortunately Checkpoint crashes for me. Do you know by any chance what's the internal encoding of pokemon filesaves (i.e.: it's json or just bunch of custom bytes?) If it's something like json I can try to diff to see what changed