The answer is C, the liability on the prior returns needs to be re calculated and agreed with HMRC
The OP actually said "c) Do I put in zero and open up the earlier years and amend these."
The earlier years' returns cannot be amended - they became final at the 1 year anniversary of the statutory filing date (i.e. 12 months following 31 January following the end of the respective tax year). HMRC cannot do "discovery" assessments as the discovery has to be an underpayment of tax rather than an overpayment.
The only way of dealing with this would be what was Section 33 TMA 1970, error or mistake relief (now called overpayment relief). The time limit is 4 years from the end of the relevant tax year, so the earliest years would be time-barred anyway.
HMRC's approach is to allow the deduction for the PAYE liability (not the interest or penalty) in the year in which settlement occurs. It has always been that way. It is easier to deal with administratively, and also means that the full deduction can be given (where it might be time-barred as above). OK, the tax rate in the year of settlement might not be the same as the relevant year(s), but that's how it's done.