Firstly I'd say chat to your accountant who should have some advice. They should know your circumstances and deal with this for you.
I believe HMRC would prefer that you are VAT registered. That way they know they're getting their hands on some taxes!
Once your VAT reg. has come through, simply apply for Flat Rate VAT (as long as your turnover does not exceed £150k), they're unlikely to take much action on their side with regard to your email to them.
Job done.
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