When I started using eM Client a few months ago I had an issue with the IMAP deleting from the server. So it was suggested that I use Local Folders. The Local Folders would not create any subfolders so I followed someones instructions to fix the issue but now I can not find the Local Folders that I wish to have backed up to the cloud and I can not find the post on this board that I followed for instructions. The Local Folders that are in App Data are empty and doing a search for the names of the folders finds nothing I know they are invisible and have set invisible searchable and even asked to show protected system files in a search. But I do not get any results. The path that shows for the folder in the tools is of no use as it just says Local Folders.
IMAP is a mirrored copy of what is on the server, so if you delete the message from eM Client it will delete it from the server. Or if you delete the message from the server using another email client or device, it will also delete it from eM Client. That is the way it is supposed to work. Moving the messages from the IMAP folder to Local Folders will also delete the message from the server.
Did you maybe change the location of your database? You can find that in Menu > Tools > Settings > General > Storage. The default location is C:\Users_username_\AppData\Roaming\eM Client.
It is not possible to just backup individual items from that folder, or at least it is not reliable. Best is to use the application’s own backup feature (Menu > File > Backup) to get a proper backup.