Console bans after transferring an account from a banned Switch to a new one? Yes. Confirmed? Well it wasn't posted here nor did they fill out a ban report form so I'm teetering on no. Not to mention said user has been suspended from GBATemp in the past so take that for what you will. Lastly, I've had other people confirm so far that their consoles have been fine despite linking an account from a banned console.
If you don't have a clean hack-free NAND backup, you may be out of luck. However if you're willing to experiment, another user wrote up a way on how to manually "clean" out your NAND which you can find
here under "Clean Up SysNAND"