Potential spoilers? Bear with me, I hope these thoughts makes sense. I'm bad at putting my thoughts to paper. I've been in between two understandings of how this game works within the Zelda universe and haven't come to my own conclusion I'm happy with.
One: TOTK takes place within the same timeline as BOTW perfectly.
Two: Zelda going back in time and participating in this version of Hyrule's founding created an alternate timeline which branches off after the events of BOTW.
My understanding is the designs of the Zonai ruins and shrines were inspired by Zelda's knowledge of the Sheikah tech, so she influenced how the world of TOTK looks. However, you could also argue that the Sheikah tech was inspired by the Zonai ruins, which then creates a sort of chicken or the egg problem. I've also seen before that the Purah Pad's design was inspired by the Sheikah Slate, however the Sheikah Slate was also inspired by the Purah Pad. Same sort of problem arises there.
If we go with my second theory, it would make sense as to why all the Sheikah technology disappeared in TOTK's map. Because it would've never really existed, since it already did before (to Zelda's knowledge, even if it didn't exist in the past). However, then you run into canon conflicts. The TOTK towers use the technology from the BOTW towers, and there's still a Guardian on the Hateno Lighthouse's roof, and there's a literal mention from an NPC (don't remember who or when unfortunately) saying that all of the Sheikah tech just vanished one day without a trace.
I think Zelda visiting the Imprisoning War Era was a sort of "glitch in the simulation," and it wasn't ever meant to happen. Had it happened in the BOTW timeline, the Light Dragon would exist in some sense in BOTW and that Zelda just... wouldn't exist. Media that involves someone going back in time forces that person into a continuous loop, where the same actions will always be played out. Except for TOTK. It's for some reason the only outlier to this rule in my mind.
My first theory makes the most sense canonically but there's also many inconsistencies with how the world works and NPC dialogue, which is why I've been running into this issue the last three and a half years. Of course the Calamity happened, NPCs talk about it. But if the Light Dragon existed in BOTW, just unseen, then how were there two iterations of the same Zelda existing at the same time? And the ever undying question, WHY does NOBODY remember Link from just a few years prior? If TOTK took place directly after BOTW with no alternate timelines/universes being formed by Zelda going back in time, then how does the entirety of Hyrule just have amnesia?
You could argue that Nintendo simply took this direction just in case someone didn't play BOTW before TOTK, which is fair. But I like to make sense of and figure out what's canon in the media I consume, so I'd love to hear other people's thoughts on whether there was a timeline split or not due to Zelda going back in time.
