Hope you have gone through GMDSS GOC renewal which details and links to relevant WPC circulars.
My understanding is that you need to pay only once with late penalty fees included, since you have to detail the same in GMDSS COP 23 form too !
Request you to upload the late fees circular here for others to refer, since I can see WPC website links are broken now. Anyways I also recommend RLO Mumbai website for relevant circulars.
Best of luck.