There was an issue that sounds similar in an older V9.x eM Client (see this thread) where if you had an eg: Gmail account and deleted an email or moved and email from the inbox to the trash folder, and then moved it from the trash folder to another label such as the Inbox or any other Gmail parent or sub label it would then only show in All Mail.
That was resolved for me in the previous interim release 9.2.1553 that has now been superseded to release 9.2.1577. I cannot now replicate that same issue again on my PC or Mac computers.
Are you using either of the above versions ?