You've corrupted your map. You need to "recover from a failed download." Everyone has done it.
First, pull the fuse for your headlights and start with a fully charged battery. It was probably the headlights being on that caused your battery to go dead even on a charger. Also, those "smart" chargers for LiPo batteries probably aren't sufficient to keep the bike charged during a download. They're more of a trickle charger. Look into a more common 5 amp charger if you still have problems.
Second, connect your bike to TuneECU. Under the "ECU" menu, go to "Recovery." That should do it. Then you'll have to reinstall the correct map for your configuration.