In Mail Archiver it's possible to combine 2 archives.

I have made 2 test archives with emails from iCloud in one archive and my backup solution Acronis in the second archive:

Archive with iCloud emails

Archive with Acronis emails

I want to import the Acronis archive into the iCloud archive. After opening the iCloud archive I select File -> Import Archive -> Internal Database from the menu:

Select Import Archive -> Internal Database from the menu

I select the Acronis archive:

Select archive

Then I need to wait until the import is finished:Import is finished

Now I have the emails from both archives in one archive:

Archives have been combined