The only use my switch has now is for my girlfriend playing animal crossing, I haven't used it myself since I bought the steamdeck. I was tempted to buy TOTK when it came out, but I've got too many games in my backlog already
Funnily enough, I had it the other way around! I copied my old drive contents into the new one with dd, but after one successful boot into the new SSD it ran into the same issue as you. I tried entering battery backup mode a few times but it didn't fix it. Only after I reimaged completely and then did a battery backup did it start working. Been good for months now though!