Hello,
It's probably worth discussing your options with your FEO. When I only had one rifle and wanted to part exchange it for another I asked my FEO if I could get a temporary certificate for the current rifle and a revised certificate with permission to buy a rifle in the same calibre. I explained that I only had the one rifle, and I didn't want to be without one for the time it would take for the variation to go through.
My FEO was quite happy with that and I was duly issued with the temporary certificate valid for 1 month and a new certificate.
Having never gone through the process before I didn't think anything of it, but the RFD I was getting the new rifle from did seem rather surprised when I showed up with the paperwork.
Regards,
Stuart