Well I'm still flummoxed a bit as I'm almost 100% sure nothing has changed since Mutt was working and now when it doesn't.
That said, I tend to feel it has something to do with Gmail organizing messages into the tabs. Like maybe Google moving messages somehow seems like a deletion to Mutt? Previously it seemed like Mutt was happy to ignore the tabs entirely, and as far as I know I haven't altered anything, but maybe Google has. I check email on Chrome on two different macs, and on an android phone. And on mutt.