Were you Outside IR35 in the past at Defra
Then you should now be talking to HMRC for Overpayment relief!
Latest stats suggest the 6% inside is now being settled with HMRC as 94% inside... meaning Defra is retrospectively agreeing to pay all appropriate taxes.
Meaning if you paid any Corporation Tax, Employee/Employer NI or Income Tax you can start to reclaim it back.
The accounting logic is... All sales need to change to owner equity. Because the money paid into the Ltd Co is yours personally not the sales. Therefore it does not attract CT. Then, to all intents your business is spending your money, so all those deductions that would have reduced profit (which is reduced with no income) need to be journaled out as use of owner equity.
The net result is you need to file new CT and accounts with new accounting logic and then ask for overpayments back from HMRC.
Then you move onto NI and PAYE as seperate conversations.