Welcome to the forum Sivasankar !
Repair of SAW fillets on 3 piece built-up web/flange connections of I or H beams is common enough... Burn-thru, misalignment of SAW heads, Skips for angular or thickness transitions and more can cause this need eh?
FCAW, GMAW, SMAW are all typical processes that might be used to make such repairs.
But you ask; "Is it acceptable" ? The answer depends on a few things you have not shared with us.
Is your production welding compliant to a particular welding code? If it is, do you have approved FCAW procedures written for repair of your web/flange connections? Do your customer contracts have any specific language referencing weld processes and procedures? and do your repairs fit into that context ?
I would say that FCAW is a good choice to make your repairs, especially if they must be done out of position.