CIS is declared on returns (for tax deducted) and EPS's (for tax suffered) in the month the PAYMENT has been received/paid, rather than the invoice date(s), so no I wouldn't say you have to account for it all in one go when your gross payment status is accepted.
Do you mean the company should claim the CIS deductions for old invoices, which have not been paid on the date of transition even they are under Gross Status in the month they receive the money?
I've always been taught that CIS is only ever declared when payment has been physically made or received with tax deducted - customers shouldn't be deducting tax from you AFTER you've been granted gross status, but if you do have any residual ones where they forget or the invoice was right on the overlap and they do take it from you, then I've had no problems putting a claim in to HMRC for it at a later date as long as there is a Payment & Deduction Statement issued.
I even had a situation where one of our client's customers refused to accept that they had gross status claiming they'd never heard of such a thing, even though it had been in place for months, and so they deducted tax anyway - there was no issue claiming it back.
I see what happened now. The company sent invoices to contractors with CIS deduction of 20% on a separate line and they have paid accordingly with the deducted amount.
We have most of the statements but not all of them. I have now to see how these outstanding how been paid gross or net. And if they are paid net shall I claim it form HMRC or to chase the contractors?
I would advise them to explain what's happened to the contractor (or if they're happy for you to speak to them about it), and if they're willing to refund the tax then just get your client to issue a credit note to cancel out the original invoice, and give them a revised invoice with the correct figures for their records.
If they are being difficult about refunding it or refuse to for whatever reason, as long as you get a PDS from them showing the tax they've taken then just put in a claim for it on your EPS as usual.
