It is reasonable to count those fixtures as "plumbing renovation," so you could still list those fixtures as pre-1993. Per p. 85 of the Reference Guide, a flushometer change out is considered a minor retrofit, and doesn't trigger the more stringent baseline.

Question
If pre-1993 plumbing fixtures are still in place (i.e. the water closets), but their flush valves have been replaced post-1993, does that count as 'plumbing renovation' or fixture replacement for the purposes of the prerequisite/credit?
Credits