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UPDATE: I got through on the helpline and they confirmed my final return can be submitted through the pre-MTD system (as I cannot register for MTD having de-registered for VAT). They also confirmed the final VAT return I submitted today using the old system has been received successfully, so no paper submission needed. Hope that helps.
I have the same problem. The old system appeared to accept my VAT return. However I am not convinced HMRC will agree even though it says "return submitted". The enquiry line is impossible to get through - it just said "Sorry, we are too busy. Goodbye" and cut the line.