I am currently working in a small ish practice where there is one partner.
I have been working on a client who owns one company (X Ltd) and half of another company (Y Ltd) and they are trading with each other. We act for both of these companies. Y Ltd submitted it's final VAT return in September 2012 and is now ceased.
When completing X Ltd's accounts this year (Oct 2012) I noticed that there is about £100,000 worth of extra Purchases in X Ltd from Y Ltd, than there was in Y Ltd Sales ledger to X Ltd (I looked on their sage to compare). Therefore, X Ltd have claimed about £17k worth of Input VAT which Y Ltd has not declared as output VAT. The complitation is that Y Ltd has now ceased.
My boss is saying just to leave it for now but I think this is dreadfully wrong! I need to put my foot down but I obviously don't want to do it too much. Also, the boss is friends with this client which makes it a little more delicate!
I really just want advice on what I SHOULD do (I'm guessing that I should amend Y Ltd's FInal VAT return with the extra VAT?) and then if it is decided to not do that should I report this and to whom?
Any help is appreciated as I find myself in a very strange and unknown position.