According to Quickbooks, have you already filed the VAT and therefore it won't let you try to do it again? If that is your current position...

1) Delete the VAT return. If you search Quickbooks Help for Delete VAT, you will find a topic on "Delete a filed VAT return". Work through that to delete the Jan-Mar VAT return.

2) File VAT, choose the option without MTD but this time tick "File Online". That should do the old-style online filing.

If that doesn't work, you'll probably have to choose a good time to call HMRC and ask if you can file for the Jan-Mar period on paper - ie real paper, sent through the post!