Backdating VAT

I have registered late for VAT and have asked suppliers to retrospectively pay their VAT, which they have all agreed to do. I have issued them all VAT only invoices. However my "making tax digital" sync up, shows me owing no tax for the backdated time, as the original invoices did not have VAT on them. And then all VAT that is now being paid retrospectively, all in this current quarter. Does this matter, as HMRC will be getting the correct money overall. My accounts package only seems to look at dates which invoices get paid, not the dates that the service was provided.

Hi Abbi Leibert,
It is important to report the VAT in the correct quarter.
If you have registered late for VAT and need to account for the VAT retrospectively then the VAT should be accounted for in the first VAT quarter.
I would contact your software provider to confirm how you would allow your software to do this.
Thank you