Hi,
If a company has issued invoices and then later raised further invoices to charge VAT then you would be under no obligation to pay this as VAT should have been charged and invoiced clearly in the first instance.
If you do decide to pay the VAT then you are still entitled to recover the VAT in the normal way subject to the normal conditions for recovering input tax
Please see the guidance below:
VAT guide (VAT Notice 700) Section 10