It sounds like you’re on normal accrual accounting so if you enter the fake invoices dated 31.5.18 but set your “VAT start date” in your QuickFile settings to 1.6.18 then they won’t be picked up by the VAT return - QuickFile includes anything from the start date up to the end of the current quarter that has not already been accounted for in a previous return, but nothing before the start date.
It won’t really matter in this case whether you enter them as zero or standard rate, either way you’ll have to adjust things back out of the trial balance you’ll be journaling in from your previous software. If you enter them as zero it’s marginally simpler as the correcting journal will just be debit debtors control and credit the same to general purchases (or whatever), if you enter it with VAT then you’d have to split the credit between general purchases and purchase tax control to get everything to balance.