Apple Mail mailboxes not working after new 10.13.4 update

I installed the new 10.13.4 update and Apple Mail mailboxes are not working. The emails are disappearing (sorry could not find another term) from the mailboxes. I have for now disabled all rules for auto filing. Even then, when I move a message manually to the mailbox it disappears. I have been rebuilding the mailbox couple of times.

Any suggestions??

Thanks in advance