I have found out the hard way that mails received in the mobile app are automatically deleted on the server.
By default for a POP mail setup the Android eM Client mobile app “doesn’t normally delete mail on the server till 7 days” as in the below eM Client POP account settings. You can however adjust this to suit. See screenshot example below.
Now if the POP emails “are not longer on the server” and only in the eM Client mobile app, then see my post from another similar thread on how you can get them back onto the server for use then in eM Client for desktop or other mail apps.
I have found that deleting mails in the trash folder removes them from the server only sporadically.
I suspect that’s some issue with your Samsung Android app. Try that same thing with the eM Client app using the latest Playstore version. As long as you have got the option enabled in the app account POP settings to “Remove from server when deleted from deleted folder” as per below screenshot below that should be all you need to do. Seems to work ok for myself when I tested it.
Note: If emails are still only sporadically deleted on the server “with both / or multiple apps”, then must be something going on with your mailbox on the server. Eg: It might have a server mailbox “read only status” at certain times of the day so doesn’t delete. Or the POP mail server might possible not be available at certain times. Unknown. Have to contact your mailbox technical support and advise that issue & that you tried multiple mobile apps.
