The safe isolation procedure is a testing method to verify the circuit you are about to work on is dead. The CU will be switched off before you remove the cover, you then test on a known live source (the incoming tails) or proving unit, then test for any voltage on the outgoing side, then back to the proving unit to verify your tester is working correctly. At this point it is safe to disconnect any circuits that will be tested. A risk assessment must be made at this point as to determine if a lock off is required, if you are alone in the house with the assessor it may not be required, if it is required you would have to lock off the main switch and not individual breakers, this is because the cover will be removed during the tests. Your assessor is there to help, just stay calm and take your time.
Any suspect readings that you have put on your EIC will be noted by your assessor, and the low reading for the IR test may become a part of your assessment, there can be a few reasons why the reading is low, neons being one of the biggest culprits. Am I right in thinking that you have just changed the CU for this assessment? The reason I ask is that on a rewire all IR tests should be done before the fitting of dimmers, lights, and neon fused connectors.
Always read up on the testing procedures, even after many assessments its always worth going back to basics.
I have just re read your post, the IR test you describe was this for the whole installation? Or an individual circuit ?