The guy at VAT online helpdesk said that there might be a communication problem with the software.
if you look under the rolled back VAT returns, you will see the following message
HMRC Responses for VAT Return
Response Date Response
28/08/2015 10:35:16 By ChRIS : The VAT Period you have entered 2015-08 for the VRN xxxxxxx was not found, please check and resubmit if necessary.
the guy said , based on this response it looks like HMRC is not reading the dates from QF.
Also one other observation. The last VAT return, the period on HMRC system is called FINAL
Whilst the one i submitted on 31st July 2015 (for the same client), the period reads 07 15
Do you think this could be the issue?