UK Amending VAT return


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Please could anybody help me with this.

VAT RETURN:


Our company (A) took over another company(B) officially on 15 February. The accounts are run as separate departments at the moment, not merged yet. By mistake, we filed a VAT return for other (B) company till 31st March 2016 (payment made already) and our company (A) (payment to be made by 7th May 2016) return for same period separately.

The correct procedure should be
Company (B) - File till 15 February 2016
Company (A) - Own VAT for 01/01/2016 to 31/03/2016 + VAT for company (B) 16/02/16 - 31/03/16

We have submitted the modified return for Company (B) till 16/02/2016. Suppose £XXXX amount to get back from HMRC as it is already paid.

But I haven't submitted modified return for Company (A) and payment is due this week. Please advise, should I submit modified return before payment (or I can submit it bit later) and set the net payment due only and HMRC will adjust payment from Company (B) payment themselves.
 
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