As far as I know, from people talking with GMs, lightning orbs turning invisible is NOT an intended game mechanic. Yes it's apparent that if you explode your own orb they will stop in place and eventually despawn. That's not an issue anyone doing hardmode Soa is having trouble with.. It's when someone who's being targeted is either lifted or mindtrapped before they can hit their orb, that it visually disappears and generally kills people. As for the green puddles in phase 1. It seems that it's a very rare case for very few people. Which can be 100% avoided by not hanging around the edge of the platform...