When damage is dealt to Phyrexian Totem, its triggered ability will trigger. A number of permanents equal to the amount of damage dealt will be sacrificed when the ability resolves. It doesn't matter if Phyrexian Totem isn't on the battlefield when the ability resolves, as long as Phyrexian Totem was a creature as it left the battlefield. If one of the permanents sacrificed is Phyrexian Totem itself, the requisite number of other permanents must still be sacrificed.