Saw the devlog. Quite unfortunate about those removals. I have the original 1.0 version and didn't see any comments about the Echo Project in the About section nor the Credits (beyond acknowledgement in the Credits)? It is ultimately your decision, though I really don't think that having them in your story "canonizes" them as being connected. They're not being referenced as real historical textbooks or anything, plenty of classes in college make you read fictional texts, especially if it was for some kind of elective/GE course. They're no more canon to the "reality" of the world than any fictional novel we might read, no one's claiming that every (or even any depending on the class) classical piece of literature we might read in an English class actually happened.
Unless you were talking about the stories being part of a more literary type canon? Some kind of worldbuilding concern surrounding what amounts to classic literature in your world? I don't think that's a major concern nor what you were worried about, but on the off chance you're worried about whether Adastra and co. are "deserving" of making some arbitrary cut to be canonized as great feats of literature/storytelling/drama/what have you in the greater context of culture in the world, I think it really should be fine. They're cute references and if you really want to overanalyze, a potential insight into the culture behind the world of Silverstone (or at least what one professor likes and wants to assign students as readings).

​Regardless, whether it's for a worldbuilding concern or a fear of upsetting an author, I suppose it doesn't matter all that much in the grand scheme of things. Recognizing the references was fun though.