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:
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:
I select the Acronis archive:
Then I need to wait until the import is finished:
Now I have the emails from both archives in one archive: