In Thursday War we’re told about the real nature of the engineers, that they’re helpful as long as that work doesn’t damage anything forerunner.
So my question is: How come the engineers aboard the Infinity didn’t wreck hell while the ship was inside Requiem? The Prometheans even got inside the ship, I doubt very much that the engineers were oblivious to everything going on.
Best Answer : 343 royally screwed the Cannon lore.
Second Answer : Engineers were brought back from Onyx and have been recovered/discovered elsewhere. Some have even communicated with humans and there may have been a mutual agreement between them and the engineers that cast this possibility out. It’s all up to speculation.
> Best Answer : 343 royally screwed the Cannon lore.
*Canon, not “cannon” 
Here’s my take: the Engineers are “aligned” with the Librarian, not the Didact. They have that purely beneficial, benevolent nature that the Librarian did her best to foster.
Note that even after the Didact’s Prometheans began attacking the Chief, the Sentinels remained on our side, suggesting that the Sentinels were tools of the Librarian rather than the Didact. It’s clear that the Forerunner forces on Requiem were not on the same page. The Engineers would, I believe it is safe to assume, support the Librarian’s goals over the Didact’s.
So they were siding with the “good” Forerunner, rather than the malicious ones.
That’s the only way I can reconcile the inconsistency. 343 clearly cares about the lore, so I doubt they’d toss it out.