Is the one energy spent when you use Automated Protocols to perform a recover action separate from the energy you use in the recover action? For example, you spend one energy to allow the recovery and have two energy remaining. You lose the two energy and get two shields not three.

I believe they are separate energy uses but want to be sure.

The energy is the cost to get the free action. Any further costs that must be paid by the resulting action is independent of the energy required by Automated Protocols.