It's from the time she was granted FLR visa.
You can apply 28 days before expiry of the probation period (ie 28 days before the 24 months anniversary of getting FLR ). I would recommend doing that just to gain a little extra breathing space.
BTW when applying for Naturalisation you can actually include the time spent in UK under Fiancee visa. Yep it's complicated.
Good luck![]()