If you just let the new OTP helper do its job, and DON'T TOUCH ANYTHING until it's ready, it works perfectly.I'm in the exact same position as you: O3DS with A9LH done before procedure revisions, N3DS with EmuNAND that I'm nervous to downgrade to 2.1.
If boot rate is your main problem, FWIW I did this, and now have maybe 95+% boot rate on the N3DS
https://gbatemp.net/threads/guide-improve-menuhax-boot-rate-to-nearly-100.410738/
I did the old pre-revision methods on my o3DS, saw the o3DS is garbage (I have the aqua-blue launch color) so I bought a new 3ds XL (metallic blue.)
The worst thing that happened was a partial downgrade from 10.3 to 9.2, which is extremely easy to fix.