Devs/mods haven't replied to any bugs topics I have talked in nor have they replied to bug reports I sent tickets in for. So I will try and help you:
You are allowed to regenerate 1000units over time, with equipment and adding gems that add 250units (yellow ones) x6 pieces = 1000+1500 so your energy can now regen up to 2500 units. With hero skills/knowledge etc you can increase this further mine is around 4500 with invader killing gear equipped. This you can use for say 10 hits that use 450 energy per hit. Then over the next 10+ hours it will regen again back to the 4500 (my max) unless I swap gear then only to what ever the new max is.
The 50000 is the max you can have at anyone time provided you use potions to fill it past the 4500.
So for me I would add 45500 energy with potions to make it 50000 then kill 3 or 4 invaders and refill again if I want to kill some more.
The other method is to hit an invader once then again just before the 1 hour timer runs out (for the sustained damage bonus) and repeat (you need a lot of regen for this method and its slow, but free).