VAT and settlement discounts

My colleague has come to me with a question regarding VAT on an invoice, I wanted to run it by someone to be sure!

We have an invoice from a supplier where we havea choice of payment terms 45 days, or 14 days less 1.5%. Our company has decuided not to take the discount and pay to 45 days terms. My colleagues concern is that the VAT on the invoice is calculated as if we will take the discount and she is concerned that she will have to enter on to our accounts system an amount that is higher than what is on the invoice and that she shouldn't do this.

I'm seem to remember that it is standard practice when issuing an invoice with a settlement discount that the VAT is calcualted as if you have taken the discount. What I 'm not sure about is if you, as the customer, are allowed to alter the VAT and pay the higher correct amount, or if you just pay the reduced VAT amount, which doesn't seem quite right!

Any advice please?