Are you using an add-on? Like TornTools, etc? I've never seen this, and can't find it in recent patch notes either.
Edit: Also, I'm guessing maybe this is on a long flight where you'll have a full E bar when you land back in Torn or a shorter flight where you spent too long abroad and end up with a full E bar when you land back in Torn? And the warning just means that if you don't do an attack or w/e abroad you won't get the full natural E regen you'd otherwise get? But, again, I've never seen this.
ah, yea is probably TTools. I see now it has a pref for CD ending notification while traveling. That said the wording could be a bit better and I've only ever seen it reference E CD and none of the others.
This is from TornTools im quite sure, and as Undo said it means that during the flight your Energy will fill up, meaning that you are wasting potential Natural E gain by going on the flight.
It doesn't really apply if you plan to do mugging, reviving, or hunting as you will spend the E when you land overseas so it will continue to regen on your flight back to torn, instead of staying full and "wasting energy"
It shows the cooldown times before taking the flight. The problem with the feature is that we have to rely on the api for it, so there is a delay on it knowing your current energy level.