As you have actually made the sales, HM Revenue & Customs will insist on the relevant VAT being paid over for the VAT period in which the sales were actually made.
For tax purposes, as an employee was responsible for the theft, the amounts stolen will be an allowable deduction. However, if your business insurance covers theft and your insurers allow you to make a claim, then only the element which relates to the uninsured loss can be allowed against tax.
If you cannot make a claim, and do not receive an insurance payout for the loss incurred then the full amount will be allowed. As the police have filed a report on the matter, you should have received a crime number, which should be kept if HM Revenue & Customs query the loss in your accounts.