Update: A few days after I had posted about this, the onboard charger ALSO stopped working! As far as I can tell there was no precipitating event: all I know is that one night I plugged it in overnight to the same wall outlet in my garage I've been using as long as I've owned the bike, and then in the morning I came back to it not fully charged and the red light on the dash was blinking. I took it to my dealer right away.
About 4 weeks later, my bike is fixed. My dealer couldn't tell me what the root cause was but they replaced both the onboard charger and the Charge Tank. I'm pretty sure if it had just been that one 100A fuse they could have replaced the fuse or even the wiring harness, so it must have been a much more severe problem. They say they are going to have some words with Zero about why this would have happened to me.
Curiously, the check engine light stayed on all the way home (no error codes on the dash) and all the way to work the next day. It resolved itself somehow while I was at work and hasn't come back. I was able to charge at home in my usual spot and also at a ChargePoint station so at least both ways of charging work now.