I did a "Clear All" and the notifications just disappeared from the extension, my Gmail mails are still unread.
I had 49 notifications upon installing it (my inbox has ~200 unread e-mails), maybe that triggered a bug. I disabled Gmail an it works now.
Clear all will just hide all notifications from Chime. Marking them as read is too undo-able, we wouldn't want users to accidentally mark a ton of important emails as read.