Make sure the Archiving scope and Archiving Settings etc is set correctly. See my post in the following thread which shows an eM Blog example of how to setup auto archiving.
When you setup and enable Auto Archiving, “Make sure you set an Archiving Scope” as in the eM Client Blog example video screenshots below, where the eg: Gmail IMAP folder scope is set to “All Mail” which in the blog example holds all the mail in the Gmail account.
Once you have then “Enabled automatic archiving” and clicked “Apply” at the bottom, you will then soon after see the automatic archive folder appear called “Archive” below your email accounts as in the blog below example screenshots.
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Also see the following eM Supports links on automatic archiving.
(eM Client documentation on Automatic Archiving)
https://www.emclient.com/webdocumentation/en/9.2/emclient/default.htm#Settings/Automatic%20Archiving.htm
(eM Client blog with video example on Archiving)
This blog explains what happens when you archive, and where the archive message go depending on what type of account you have.
https://www.emclient.com/blog/archive-your-emails-easily-with-em-client-315
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