So, from Chapter 1090, if we take it, read as written, York's "My brain isn't synced to all of yours" implies the syncing is always happening. She's just able to disconnect and no one noticed, or partially disconnect and no one noticed. Fact--she wasn't continuously syncing once she started her plot.
From Chapter 1108, we see the room where the mechanisms activated. Them going to punk records was already a bad move in that sense. The room they blasted wasn't the same as the source/activator.
On the note of why York didn't know anything, it's pretty simple to logic out.
Vegapunk seperated aspects of himself into the sattelites, so they just reflect the one distilled quality. There's a lot of interesting things to take away from this, such as Vegapunk tilting more toward negative aspects than positive, but I digress.
Everything York is capable of, Vegapunk is capable of. If she is wise enough to desync, so is Vegapunk.
Another point to take note of is that the ONLY sattelites involved in the message were Good and Wisdom, the one positive aspect, and one of two neutral aspects.
These three seem to have never synced the events of that day, and they actively witheld it from the negative qualities.