If the client won't let you sort out the borrowed neutral then your only recourse is to put both circuits on one MCB and make a note on the EIC. Not ideal, but as long as the load isn't going to cause the MCB to trip then it will at least be safe. The downside of this is obviously that in the event of one RCD operating, you will lose all lighting.
You do need to fill out an EIC for the CU change, there's no getting away from that, and then if the client wants an EICR as well, this will be a separate report. At least if you do it at the same time, you will already have the readings for your schedule part.
I can only stress that if you make sure you do some basic pre-change tests before committing to a CU change, you can save yourself a whole world of pain later on, as in this case.