As the title suggests, EOS is glitching after the first phase. He will reappear not only fully shielded, but with 100% health as well. After disappearing again, he will not reappear.
After killing him, whatever he awards on the second vomit - whether Legendary or not - will disappear when vending those items.
Ok, for me, the first bug is caused by having another toon in the chamber with the vendors before you enter the boss area (say, a mule i have join to take gear and then leave) and then entering the boss zone without saving / quitting / reloading first.
On my system, at least, i have tested it and that is what causes the first glitch 100 percent of the time.
He stopped glitching for me when I didn’t re up ammo from any containers forward of the big platform at the end( the one next to the exit that appears when you beat him. I only resupply from the crates where you first come in). Killed him <20 times since then. No glitch.
Mysterious and annoying but less annoying than the regularly freezing I experience with this fight. Save & Quit is better than having to Restart your system.
When you first enter, look at the large platform at the other end of the board. I don’t resully from the ammo crates on that side. I only resupply from the crates on the side you first enter from.
I only ever resupply from the vendors just before the fight or the timed restock stations immediately around the octaganal island jump pad “safe spot”.