I think, get in touch with him straight away and give him the full picture.
A CO has to tick the boxes for evidence he has checked, and obviously there is one saying 'birth certificate' (which ideally will show the true birth date, but this isn't an ideal world!). What you're trying to do is help him tick the box in some acceptable way. He has no reason to be angry at you because of the difficulty, which is not of your making, and if you keep him informed of what you're trying to get through other agencies, so much the better. They only get a bit hard, usually, if people expect them to be mind-readers.