Permanent Residence for non eu member of eu member

Hi guys.

Things are a bit more complicated due to brexit thing now and hard to understand what route to apply for now.
let me explain our situation and if anyone had the same experience please show us the way out.
we need to apply for permenant residence for my wife now.she had residence card 5 years ago and now due to expire .
she is non eu member of eu family member and we have been married for 5 years in the uk .do we need to apply through paper application way for eu family members or is it going to be this new settlement route? i am abit confused.
my other question also will be that i was eu citizen 5 years ago when we applied for her resident document but now i am also british citizen. is it gonna make an affect on the eu route application for her, what outcome should we expect in this case.
if anyone have been in similar situation please advice us...