I fixed my partial downgrade problem. For anyone else in this scenario just rerun SystemUpdate and downgrade again.
Worked fine the second time. I have injected FBI and am dumping my systemnand with emunand9 now.
EDIT: was a partial downgrade, fixed by rerunning SysUpdater and downgrading, worked without a problem and everything seems fine now.
I have an N3DSXL that was on 9.8.0-25U
I downgraded to 9.2 but never seen the native firm or reboot warnings. It was installing a couple CIA's for 20-30 seconds...