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,
Unfortunately, we are unable to provide specific advice tailored to individual circumstances on this forum. This forum is for general queries only and is intended to help you self-serve.
Please contact HMRC on VAT: general enquiries 
Thank you