How much of the deleted Skaianet lore is still canon? I doubt any of the stuff about Hitler will ever come up in-game (they aren't *that* dumb) but it also seems like Calamity is probably a major player who can't be written out because people were offended by the history that mentioned her. Yeah this question is phrased very clunky but ya know what I mean?
i don’t think the exact word for word content of the systems files are ever going to be canon, but i also dont think that was ever the intention. they were more of an internal “guideline” for how the different elements of the homestuck universe come together, and how these different elements could be explored in future homestuck content. obama in the epilogues being obviously the same obama from the skaianet systems, for example.
like you say, some of the parts of these documents are more important than others. whether it’s “”canon”“ or ““not canon”“, the stuff regarding world war 2 can be glossed over with no effect on the overall story. but calamity serves as a major motivating force for the condesce, who is in turn a major player in both homestuck and hiveswap’s worlds. since the skaianet systems stuff was probably never intended to be published as any kind of standalone text, there’s no doubt she was created for some other purpose, and i think hiveswap is as good a guess as any as to what that purpose could be.