HMRC have the power to withhold repayment of R&D tax-credits until they are satisfied with all the details of your claim: the numbers, R&D projects (or technical narrative) and the supporting methodology.
If HMRC have any questions about your claim and its preparation they may open an enquiry. In an enquiry, the usual 28-day payment-processing procedure will not apply; HMRC will instead withhold the repayment until they are satisfied with the claim and they have reviewed any additional information they require.
During the course of the enquiry, as aspects of the claim are discussed and agreed, you can request part-payment to reflect the amounts within your claim that have been agreed upon. When the enquiry is concluded and HMRC are satisfied with the claim, any further amounts will be paid – including any interest accrued.
HMRC may also open an enquiry into your R&D tax credit claim after the claim has been processed and paid. In this case, if they are unsatisfied with any aspect of your claim, you may have to pay some money back at the end of the enquiry.