A short in the lighting circuits would pop a fuse. That would be a separate issue as the charging system isn't fused.
I suspect you have a loose connection between the alternator, rectifier, regulator or battery. Check all the big, multi-pin connectors under your side panels. If all is tight, then there is prolly a failure of one or more of those components. Did you ever try to jump the bike and accidentally got the jumper cable reversed?