Its crazy with all the permutations that are possible.
But as long as his CAAS license is valid and up to date, I see no reason why he will not be issued with the FATA.
FATA is based on a valid ICAO fligh crew license, it will not matter how his CAAS license was obtained in the first place.
I know of an Indian FO who went overseas to convert his DGCA license to ICAO.
Cleared ICAO ATPL. Came back to India and got a FATA issued on the basis of that ATPL. He is now a captain and is attempting to clear the DGCA ATPL conversion exams.