When a character is drained of one or more levels, they determine all their stats according to their new, lower, level. This includes hit points, which is the issue of confusion here. Since hit points aren't a static number from a table, but rather a variable one determined by rolling dice each level, how are the hit points for a drained character determined? Should players keep note of how many hit points were gained on each level in case of energy drain, or are their hit dice rerolled when their level changes?
If they are moderate to high level (5th level or more) I have them roll one Hit Die and subtract that number of hit points. That's an imperfect method for low-level characters though. It's better for them to roll hit points again.
I am not an Autarch, but I have a spreadsheet where I keep track of each PC's hit points as they level for just this reason. When they earn a level back they roll their hit points for the "new" level again. If some kind of restoration magic was used to get the level back I might give them their old hit points back again, but that has not come up yet.