One eyed jack many people have complained about this bug and I just experienced it for myself I was doing the battle and after defeating the colored heads the ebon head disappears and I didn't know what to do so I tried defeating the colored heads again but still he is gone I can see him I just can't attack him and I can walk on the square he Is on and he is just invisible basically I can't do anything or move unless I beat this quest can you please fix this bug many people have reported this but the bug is still here please read this and fix the bug.
Also, sometimes some of the Hydra heads respawn in already occupied spaces. It may be a little hard to reproduce, but it is very annoying when a respawned Scarlet Hydra pops up on top of the only Cobalt head that I need to kill.
Still finding this bug. I have only done the hydra 3 times, and the 3rd time I encounter the bug. 33% chance is not that hard to reliably reproduce, obviously. I didn't know it was a bug, asked a friend to come, he knew right away it was the bug, he has encountered many times before.
I am lower level, not in Aquila yet, ported to friend who was in battle during the stage where we had to kill 3 colored heads. The Ebon had been there before I ported in, but was never hit once and has never reappeared. We've almost got the entire board full of hydra now. :D I killed several hydra with vengeance and blade storm, then got surrounded by ice. Bonnie was the last crew member to have a pop up message with some instructions, but it disappeared before I could read it. There was no audio voice over with her message. We've tried to kill as many as we could, to see if maybe Ebon had somehow spawned under anything. As far as we can tell, we just can't see it anywhere.
I'll submit a bug report with the funny screen shot of a nearly full battle board, along with relevent portion of Captain's Log, starting from when I ported to my friend.