Broad description of how the game got here: Chelsea started near the Concrete Jungle, I moved to contain her along the Rodden-Industrial-Winfield line. Around day 2, after containment was fully in place, I got the "Don't bother engaging Chelsea" notification (at the time I got this notification, I didn't actually have vision on her).
Day 3, I have unlocked shredder rounds and I'm scouring the contained area but I can't find her. News reports on her have also stopped for some time (I tend to tune them out so I'm not sure when that happened).
In what may or may not be related to the Chelsea thing- Peak Point has an extreme level of infection but no actual signs of infection. I also lost a helo pad at ellens point and possibly a couple other structures to enemies I was never able to locate by air.