Hello FFG forums.
The Energy Shells action wording is a bit hazy. I think the intention is if you perform the action on the energy card to "reload" the card (reload instruction), you suffer the effects from performing a reload action by getting a weapons disabled token.
However, the RR only describes how the Reload action works (1, choose ordnance, 2 recover charge, 3 get weapons disabled) and that a "reload" instruction is not a "reload" action. I assume you get a weapons disabled from a "reload" instruction, but the rules can be explained in 2 ways.
Option 1) You have a reload instruction for the card, which is not a reload action so you do not follow the steps for reload action, flip back the charge
Option 2) You have a reload instruction for that specific part of ordnance, then follow steps 2 and 3 for the "reload" action.