We faced the same problem a few years ago and it is best resolved by writing to HMRC Tax Office and explaining that you want your house declared your principal private residence and that you would be living in it subject to the exigencies of the Service. You will be sent a letter and treat this like gold as HmRC record keeping seems to be lacking. You can flip-flop your PPR between different properties (as the MPs did) quite lawfully to avoid CGT. Just keep meticulous records of all expenditure and income. The way we have down it was based on running a non-public fund at Lyneham many moons ago, but updated to running a spread sheet showing income and expenditure - the latter broken down into the areas required by a Tax Return ( eg insurance, maintenance, administration, finance charges, capital improvements and so on). I'm sure there are proprietary software packages, but there is no substitute for maintaining a ledger and scanning all expense receipts.
Of course I can't give you advice - this is simply an account of our experiences that is simple and workable - and has survived two HMRC Audits