There is a correct method for adding something that was omitted and it certainly is not by adding anything to protocols that are signed off. There is a standard pharmaceutical industry method that has been in use for many years.
It is by raising a Supplementary (IQ, OQ or PQ), and treating it as you would, a new IQ, OQ or PQ.
In this SIQ (for instance) you give your justification for raising the protocol along with a rationale on the implications of it being required.
Because this action (test or inspection) was not in the original protocol, so the original system/equipment was never verified as being compliant for this requirement. Was there a risk that this could have produced or allowed to be produced, damaged product.
If there was a risk to the product, what have you done about product that was produced prior to this supplementary validation verification.
These points need to be rationalised and justified in the introduction chapter in your Supplementary Protocol.
I went into a plant and found the validation protocols so poor, that I had to rewrite over 100 iq/oq/pq’s. All were done as supplementary protocols.
The regulator held that the original documents (although crap) were approved company protocols and applied to product that was produced when they existed and so could not be simply discarded.
Ensure you have traceability by cross referring original and supplementary. Do it properly and it really is no big deal, regulators, generally do not give you a hard time for sorting out your own mistakes, as long as your efforts are genuine and honest. Deliberately fudge it, and they will crucify you.