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do you see it in the log that there is something wrong or where do you think emails get not deleted?
please turn the project status to "active (email verify only)" and run it.then post the log.stop and restart it and post the second log.
see this line...00:00:53: [ ] No E-Mails to read on this account. Make sure you do not check/delete emails using your E-Mail-Client/Browser.It showy that emails are getting deleted correctly. Why your browser shows the emails as unread is something I can not tell but it is working as expected.