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HMRC Letter re Late MTD Return

Client received letter re VAT return not filed - I have electronic copy with HMRC reference

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This morning my client received a letter from HMRC stating that the annual VAT return for the year ended 31 August 2019 had not been filed and issued an estimated assessment.

The return was filed using the IRIS VAT Filer and I have an electronic copy of the return stating: -

a) Processing date - 31 October 2019 (The last day for filing as it is an Annual VAT return); &

b) Form Bundle Number - As generated by HMRC at the time of filing.

On phoning the agent helpline they claimed they had no trace of the return and that I need to now filed a hard copy return which they will e-mail to me print out, complete and return by post.

Has anyone else encountered such issues with the MTD filing service, any advice most gratefully received.