In the past I have created a VAT return (Report) and the made adjustments to that to re-claim VAT. Now I have registered for MTD if I make an adjustment Quickfile tells me that will not be reported to HMRC.
Most of the re-claimed VAT comes from receipts - not from purchase invoices. Where do I go from here?
With MTD the reasoning behind it is to have a complete digital audit trail. If there are figures adjusted then there is no digital trail for these adjustments. This may be why you are unable to submit your amended return.
To submit from QuickFile you can use the bridging module - if you have a spreadsheet with the figures you can enter the figures manually.
Alternatively if you record your full accounts through QuickFile then QF will create the return for you. If you are having to manually adjust each time then there will be something you are not entering through QF. You may wish to start entering this data properly in order to account for it in your VAT return.
All the message means is that the adjustment amounts themselves and the notes you provide won’t be submitted to HMRC, they only get the final amounts in boxes 1-9 after the adjustments have been applied. This is no different from the old system, it’s just been made more explicit in the user interface.
HMRC explicitly do allow manual adjustments under MTD for things like partial exemption calculations that you can’t do as you go along (ref). However:
it would probably make more sense to record these transactions as purchases anyway, so QuickFile can account for them without the need for adjustments. Can you explain more what you mean by “from receipts, not purchase invoices” so we can suggest the best way to enter them?