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Please speak to HMRC or a Tax Specialist Accountant about this. You should only be "unfiling" a VAT return on QB if recommended to do so by HMRC or a TAX Accountant.
It's crucially important that you speak to HMRC if you have filed the numbers of your VAT return with them, and they are matching.
You can refer to this article to get in touch with our support team: How to get help with QuickBooks to request the period to be unfiled, once confirming this is the correct thing to do with the proper authority figures (HMRC/Tax Accountant).
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