Out of bankrupcy comes new ciaos

I am bookkeeping for a company that has arisen out of a multiple jumble of bankrupt companies. HMRC has placed the new company under a ‘compliance investigation’ as inadvertently, suppliers are still using several of the old company names, as they are close to the trading name of the new company. I have a start date for the new company and have gone to each supplier to request invoices be addressed to the new company to comply with VATREC5010 regulations as effective 1 October 2007. Each supplier has received the New Company details and letterhead. As such, most have complied and issued new ‘copy’ invoices with the correct trading name. One supplier has refused due to ‘unable after processing’ (account is fully paid by New Company). This leaves me with a small batch of invoices value £3 749.28 with 5% VAT of £187.46 in limbo. Alas, they are already written into the accounts of the new company, as they had to be paid. What is the best way to resolve this issue to comply with hmrc, as it is only one sample of name issues that I am now obviously faced with.
Note: The ‘New Company’ is trying to pay ‘essential suppliers’ from the bankrupt companies (hence the name problems) to keep them available now as the new business grows, is this within itself acceptable practice?