Thanks for posting on Community Gillwill.
If you have signed up for MTD with the HMRC you won't be able to file on the HMRC gateway using the old method. What you can try is removing the last filing as when something is paper filed in QuickBooks Desktop this is only marked as filed and not submitted with HMRC. To remove the filing go to Supplier Centre then HMRC VAT locate the last filing go into the filing and select delete. This will then un-file for this period and allow to submit via MTD method.
We would strongly advise speaking with HMRC to confirm whether you have signed up for MTD before following these steps.
