Last I tested it, it worked as intended. The healing state lasts 5-6 seconds and then turns off on its own. Does the boss get stuck when this happens?

It doesn't turn off after 5 or 6 seconds, no. I do actually have weapons that I brought that do a lot of damage and broke the part in a matter of seconds, but it just stays like that afterward and I can't do enough damage to harm it further. I ended up spawning in a dev gun and killing it that way so I could see the mission through. I'd love to fight it properly later. I can try fighting with less damaging weapons and see if that does something different. I know the Ixodoom gets stuck sometimes when damaged too fast. Aside from that, which is probably a conflict or error on my side, this new dungeon is solid. Worth the wait. I just wish I knew what the trigger is to get Akaggy to start the 4D mech upgrade quest. Don't need to know where it is, I just need to know what type of trigger it is. Prerequisite, item pickup... But yeah, off topic. I can test that later and get back to you.

Getting back to you on this. I just tested using a weak enough weapon so I wouldn't kill it quickly. I have two potential hypotheses.
One, damaging it too quickly at any point may cause this. This may require further testing.
Two, I noticed it underwent a superheal while all parts were present at the start. Disrupting its cycle before this point by destroying one of the parts may cause this issue. I did kind of open fire as soon as I went into the room and saw something I recognized as a target.

Now that you mention it I remember encountering the same issue when the boss is damaged too fast during its intro animation. Admittedly since it is a tweaked version of Big Ape fight, it retains some of its problems. I'm not sure how to fix this bug yet, so until then I suggest letting the boss do its thing before it uses its first cryoblaster attack. If it stays invulnerable and/or stops attacking, the player can warp back to the checkpoint with admin commands, this resets the boss.

You should be able to start dr. Akaggy's new quests after completing the Advanced Test Drive. There are no other conditions.

Originally posted by Angry Turret:

Now that you mention it I remember encountering the same issue when the boss is damaged too fast during its intro animation. Admittedly since it is a tweaked version of Big Ape fight, it retains some of its problems. I'm not sure how to fix this bug yet, so until then I suggest letting the boss do its thing before it uses its first cryoblaster attack. If it stays invulnerable and/or stops attacking, the player can warp back to the checkpoint with admin commands, this resets the boss.

You should be able to start dr. Akaggy's new quests after completing the Advanced Test Drive. There are no other conditions.

Ah! There it is! I neglected to check my quests! The character was still on "Parts and Labor"! Silly me.
Happy to help, if I did. Sorry to bother, if I did. Wonderful content. Great stuff.

@Naii Starwing Just to cover our bases here, you wouldn't happen to be using this mod at all are you? It's notorious for breaking bosses like Big Ape and whatnot

Originally posted by Armok:

@Naii Starwing Just to cover our bases here, you wouldn't happen to be using this mod at all are you? It's notorious for breaking bosses like Big Ape and whatnot

I... am. Why would this be doing that?

Originally posted by Naii Starwing:

I... am. Why would this be doing that?

It overwrites the monster.lua file, which breaks certain vanilla and modded bosses (as well as causing other minor bugs with monsters in general). It's not a good mod to be using because of that issue.