I would think it best to disconnect the power supplies from the blown channels. There are several different sections to a power amplifier channel and some of them are probably still working - let's assume the power output section is out for a second - and the working sections that are active will draw power. If part of the circuit is damaged, it isn't good for the working part to be operating into a non working section - just my opinion. I would disconnect the non working sections if it were me.
Brad
Brad