The mail content is not the issue, as I have all the files I could just import those if it were just about the content. It's the meta information I'm after, mostly the folder information (the mails were stored in a complex hierarchy based on customer relation to quickly find them if needed). And according to the documentation the GXMT format is the only one that can import/export those information. If I could import/export single mails with all meta information (I mean folder and flags, not mail header) that would be of course a lot easier, but that feature doesn't seem to exist.
So what I need to do is: Load the youngest backup, index the mails, then load the previous backup, than see what additional mails are included and merge them into the existing backup and so on. And in the end have look what additional mail still exist as files only and import them without folder information.