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"Total Energy" is actually the energy with which you start a Sky Combat.
During combat, your energy can sometimes increase above your starting energy. When that happens, your "Total Energy" is not modified. Standard attacks and attacks based on your main cannon will increase proportionally if your Energy goes above your "Total Energy" but the damages and cures that are explicitly a percentage of your "Total Energy" will not.
Because of that, "Total Energy" is actually a misnomer and a more accurate term would be "Starting Energy". The term "Maximum Energy" is also sometimes used unofficially to designate Total Energy, it is however just a much a misnomer.