The rules about VAT on charitable buildings are subtle and it is probably worth their while getting advice from someone who specialises in charity VAT issues.
However in general a NEW building for charitable non-business use can be zero rated for VAT and it sounds as though this should apply to the toilet building. It’s not a question of reclaiming the VAT – it’s about getting the builder to appreciate they can invoice for the work with 0% VAT on the invoice (instead of 20%). The charity (the PCC if it is an Anglican church) will need to give the builder a ‘Certificate of zero-rating’ – so they just need to send the builder an official note preferably on the church letterhead confirming that the building is for charitable non-business use. (Non-business means not generating trading income through lettings or other chargeable services.) But to do this it is vital to get the builder to invoice the toilet block separately from the vestry work.
However, refurbishing an existing vestry is clearly work on an existing building, so this would generally be subject to standard 20% VAT. Having said that, if the church is a listed building, there may be scope for the PCC to reclaim some or all of the VAT on this work under the ‘Listed Places of Worship Grant Scheme’ – see
https://listed-places-of-worship-grant.dcms.gov.uk/ In general this is for repairs, rather than improvements, but often these refurbishments encompass at least some repair work.
But please treat these comments purely as pointers to issues for consideration, not as formal advice.