I'm not sure I follow you, unless you mean to say that you claimed a % of the mortgage interest + % of the rates & insurance + % of the depreciation for the floor area of the bedroom rented and these deductions were greater than total the amount you received in rent, and therefore you made a loss that entitled you to get some tax refund. Is this correct?
For the amount of accounting that you now have to do, it was probably not worth claiming like you did.
Firstly, you could have just had an arrangement whereby this renter just contributed to the household expenditure and under these arrangements any income you received would have been un-taxed. (especially since it was mates rates anyway).
You have to work out if indeed there was any capital gain in the 6 month period that you rented the room out for a start (so valuation at start and valuation at end) .....and the rest I'll leave to the accountants to advise you on....they have the formulas for it.
You have to apportion the gain according to the time you rented the room and the proportion of the home rented. So if you had a gain of, say $50k, and you sold after owning it for 2 years, I think it would be something like capital gain $50k x 6/24 x 0.2 (20% of the house) = $2,500. Then there is the 50% CGT discount, so $1,250 to pay. Does that sound right?