Mail filtering in macOS Sierra
Sounds like you may have accidentally turned on the Message Filter, which hides read messages by default? If so, you can turn it off again with View>Disable Message Filter, or hitting Cmd-L.

(I only found about this feature a couple of years ago when I accidentally turned it on in the default layout, then switched back to Classic layout. At that time, the filter setting carried over, but there was no indication that the filter was turned on. In High Sierra, it appears they've avoided this problem by disabling the filtering capability in Classic layout.)