You would need to submit a BR application if the works were "not" carried out by a registered FENSA installer. If you have had the works carried out (which I assume as the BCO has asked you submit a Regularisation certificate), then you should be able to present the certification as provided by the FENSA installer, which will be enough to satisfy the BCO.
Can you explain exactly what you mean by “replacing windows with a door? If the work that’s been done involves cutting down the window line to the floor, the FENSA self certification remit doesn't the building works involved with that. You will still need Building Regs. approval for cutting the hole & making good & LABC will want to know/inspect how you closed off the reveals & made good the DPC/membrane in the floor.
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