There is a way to get it to work as we use an o3ds 2.1 ctrnand even when on a n3ds for the current A9LH guide. It's just that it shouldn't be done as it doesn't fully work properly and can cause many issues (like letting a n3ds with 2.1 go to sleep can permanently brick)
So it may be possible but shouldn't be done until there is a tutorial about it and people with hardmod have tested it.
As for OP if you have A9LH you can either restore a backup or download a n3ds 9.2 ctrnand image from the Plailect guide and auto transfer that to fix your problem.
These new ctrnand transfer methods theoretically allow you to transfer a majority of the NAND from one 3ds to another, but as for moving it from o3ds to n3ds and vice versa that's a no-go afaik.