I use the restore tool and the mail back up is restored to eM Client mail, but only for a few seconds before it disappears and reverts to the current mail.
This happens when your email account is setup as IMAP. That means that the server is the primary storage and will always overwrite the local cache.
If you want to recover messages that were previously cached from the server, but have since been deleted from the server, disconnect from the Internet before you do the restore. Once the restore is done, move or copy the messages to Local Folders, and then reconnect to the Internet.
Once the sync with the server is complete, you can move the messages from Local Folders back to the regular folders and they will be uploaded to the server.
If Local Folders are not visible below your other folders, enable them by selecting Menu > Settings > General > Show Local Folders.