VAT is charged to the person (not business) ie self employed, company etc. That means your company and your self-employed status are treated differently as long as there is no linked activities.
VAT is compulsory if you exceed the threshold (over 12 months period) or at anytime your sales in the next 30 days exceed the threshold. It appears you will be caught by the later. However since you are not expecting to be paid why not invoice when you know you will be paid. Alternatively you can join the cash accounting system where you only account for VAT when the invoice is paid.