Once again, my answer is dependent on the applicable welding standard. The query didn't state what welding standard he is working to.
My reply is based on AWS D1.1, which may not be applicable. AWS D1.1 does not recognize GMAW using the short circuiting mode of transfer as prequalified. Therefore, a PQR demonstrating the ability to develop the mechanical properties required is necessary. Both the SMAW and FCAW processes are prequalified, thus no testing is necessary to use either SMAW or FCAW welding processes.
The original PQR utilized both GMAW and FCAW. I made the assumption that GMAW-S was used for the root and FCAW for the fill. That assumption may be wrong. Again, too little information was provided to know for sure.
SMAW can be substituted for the FCAW because both processes are considered prequalified. Again, the assumption is that all the other conditions of prequalification have been met. Whether or not all conditions of prequalification were met is a big question. Again, not enough information was provided to know for sure.
I do know that if ASME Section IX or API 1104 is the applicable welding standard, all bets are off!
I would be easier to provide a better answer if all the pertinent information was included in the original inquiry.
Best regards - Al