Might be worth calling up comsec and seeing if they're able to just remove SP1 from your portfolio. Obviously if it stays there it just will continue to give you enrroneous portfolio figures. It sounds like its stuck on the last traded market cap which clearly is not accurate. SP1 is now a shell arguably worthless.
In terms of CGT, its tricky as the assets still exist just not in that entity anymore, technically you still own your share of the assets in the new Cypriot entity. You should seek advice about how you might go about claiming any losses, if any.