Hi Laura,
If you are converting 2 flats in to one dwelling then you can benefit from the reduced rate of VAT for the majority of the work.
Please see the guidance below:
7. Reduced rating the conversion of premises to a different residential use
It would be for the suppliers who do the work to charge you the 5% VAT where appropriate to the work carried out as unforunately you would not be able to claim any VAT from HMRC.
There is a DIY Scheme which HMRC operates but this is only for building a new dwelling from scratch or for convering non residential properties in to residential dwellings.
Please see the guidance below:
Claim a VAT refund for a new home or charity building if you're a DIY housebuilder.
Thank you.