We’ve now done payroll and p60 for 18/19 tax year based on basic salary to NI threshold. This has now been accepted and funding reinstated once I had reapplied, they have said they will need to see evidence each quarter of earnings, so have agreed with Accountant that payroll will be run once a quarter, which will provide HMRC with the evidence they need on a quarterly basis.

Hope  this helps

I’m having the exact same problem! Husband company director of newly formed ltd company in 18/19 tax year, self assessment not yet done, but they are still basing earnings on that of him being a sole trader and his return for 17/18.