Running a battery down until it won't go anymore then recharging really is not good for it. I can see IF you have some really awful problem with it, but being close to zero without pounding it and kicking it into the ground, should be plenty for a a bms to retune itself.
i do not recall the energica's wanting you to run them to zero to recalibrate. typically topping them off can reset them, and if it won't hit 100 percent a few 'restarts' of the charge cycle should walk you up to the full charge point. Again, id not recommend running it, or any battery really, down to zero, and especially pushing it to it does a safety shutdown, then restarting. THAT is why it wont charge anymore, you pushed the voltage so low, the pile crashed and it's too low for the bms to let it back online.
This may sound goofy but if you do manage to brick a battery that bad, sometimes what might save it a bit w/o tearing it open is. IF you can get the bike to turn on at all, or any connectivity to the battery, do a manual regen, heft it up on chocks or whatnot and spin the wheel to gen some power back into it, could be just enough to get the voltage to come up just enough to wake up the bms to let you charge it normally. I have to do that to my lawn mower sometimes, the regen puts just enough power into it to charge up the bms to wake the bastard back up when it's tripped out hard. it might work for a bike too but no guarantees.
aaron