I posted previously about this same issue. Occupancy clauses are being flouted up and down the country. I personally come across 2 or 3 instances every year, and I am sure my experience is not unusual.
I am 100% in Vanilla's camp on this, and I would not certify title to a lender where the occupancy clause is not complied with. Clearly, some solicitors do seem to feel that it is ok to certify title without there being strict compliance with an occupancy clause in the planning permission. Rather than argue the merits, whenever I have a client who wants to buy such a property, I simply tell them to use another solicitor. If our planners ever get around to enforcing these clauses, I have no doubt that there will be people very quick to blame their solicitors for letting them go ahead, but the reality is that they will only have themselves to blame. Mind you, I doubt that the planners will ever get around to enforcement.
(this is not directed at original poster, who seems to be in the "genuine case" category, and who should, I rather imagine, be able to get the necessary clearance from the Council)