When you’re on flat rate you shouldn’t itemise the VAT on your purchases at all - I suspect you’ve entered some purchases with itemised VAT before you turned on the flat rate mode (which hides the VAT column unless you specifically tick the box for a particular purchase to say it’s a capital expense over £2000 where you’re allowed to reclaim VAT).
You’ll need to first disable the flat rate mode in your VAT settings, then edit any purchases where you have previously itemised the VAT to put the inc-VAT total into the “net” column and “no VAT” in the VAT rate. Once the purchases are cleared up, turn flat rate mode back on.