I'm guessing that at the moment he is receiving something like this..
http://www.direct.gov.uk/en/MoneyTax...me/DG_10018923
The way I understand it is... If a second adult moves in who is not entitled to any benefits (eg a non-British national under immigration control), then none of this benefit would be paid any more as the second adult is deemed to be capable of paying the full bill, even if that second adult wasn't actually earning. If your joint income was low enough and you could claim income support as a couple you'd get the council tax benefit back. Unfortunately if you only have FLR you can't do that or else it will cause you problems when you come to apply for ILR.
Please inquire again, though don't be surprised if this is what they say.