Apple Mail Inbox shows all messages unread but they have been read.

Hello Gwynedd,

You may find a helpful step for marking all of the emails as read here: Mark emails as read or unread in Mail on Mac

In particular, check out this step from the page:

If a mailbox in the Mail sidebar contains unread messages, you can easily mark them all as read. Control-click the mailbox, then choose Mark All Messages As Read.

This should help resolve things, but if not, it may also help to try manually quitting the Mail app (Command-Q or Mail menu > Quit Mail), and relaunch it.

For odd issues that come up, it can help to try restarting the Mac as well, if you haven't yet: Log out, sleep, restart, or shut down your Mac

From the link:

1. Choose Apple menu > Restart.

2. Press and hold the power button until you see options, then click Restart or press R (or use the Touch Bar).

Cheers.

Gwynedd,

Thanks for replying back. We’re glad to see that the issue is resolved after restarting your Mac.

Have a great rest of your day or evening.