I just had this happen this morning! [macOS 14.5 / Mail 16]
Happened to all 7 mailboxes (gmail and Apple), all 6 colors.
I've havent had this issue before- even after all of my previous (30yrs) of OS and processor upgrades.
rebuilt mailboxes, restarted, no help.
edit: just looking through my mailboxes it 'seems' ALL 'business related' emails have disappeared from my inboxes?? but personal emails (person to person) emails are still there. Also all my SENT business emails are still there—only recv'd emails are missing?
edit2: OK, it seems 9at (least for my accounts) its Google/gmail account related. for some reason on the gmail webpage many of my inbox emails were moved to "catagories" folder. NOTE: I don't use any 'categories' or 'labels' via gmail account and access ALL my mail via the Apple Mail app.
After going in to each account and bulk 'move to inbox' and also erasing any label/categpory. I now have all my emails as before. BUT, ALL FLAGS are now gone. its not great, but at least I have all my business emails back in the inbox as before.
edit3: alls NOT well, seems my Mac has been corrected, but my iPhone 12 Pro iOS mail acts have nothing in the inbox since 2013??? tried, restarting, log out/in, force update folder. not will repopulate my mailbox in the iphone (though all of the mail is visible in the accounts on the Mac,
iCloud.com, and Google Gmail-page. Maybe this is a iOS issue?