Using eMClient since 2013 and several times it happened to me that some old emails form an  inbox folder disappeared (I noticed it very quickly because I always have them on the top of the inbox folder).
Fortunately, I have backups on several places but uncertainty remains. I use pop3 protocol and the mail servers of the local provider, pop3 is set to leave copy of messages on the server and remove message from the server when deleted from trash.  Automatic archiving is off.
The problem may also concern other email folders but the  inbox folder is the busiest and the other folders most likely completely refresh after recovery of eMClient data folder.