In a recent court case, the Court decided that if VAT is charged on an invoice, this VAT is due.
The case concerns a taxable person who operates a consultancy for job placement, recruitment and selection. The corporate income tax returns states other amounts in turnover than in the VAT returns. Therefore, the tax authorities raise an assessment, based on the turnover reported in the annual report. The Court looks at the invoices that were issued, and the VAT amounts that were charged on these invoices, which it eventually takes as the correct amount of VAT due (and thus not the amounts mentioned in the annual accounts).
Source BTW jurisprudentie in Dutch