Thanks Ashleigh1 .

This is a very helpful post.  It has solved my problem too (April 2024)..

I have followed your advice and logged into the HMRC portal,  and found the "VAT period" setting on my VAT account.  Job done! 

I think it would be very helpful for many people  if info relating to this issue  could be flagged within QuickBooks Online VAT Settings (Edit) area.  I have been struggling with the issue for over a week in response to a letter from HMRC.     But clearly once MTD is enabled,  this setting within QB is ineffective/disabled.

Another al;tentative would be for the VAT period setting within QB to be "greyed out" along with an explanatory note to refer to the HMRC portal instead.