An update.
I followed the same instructions as you have linked to and ran it as a batch export for all mailboxes at once. The mailbox I’m having issues with was the smallest so I started to run the import on that one. I finally got the others exported as well and ran the import of them and for those it went well, at least kind of. When I run du from MailDir I have ~500 MB from a mailbox of 1.3 GB and 1.4 GB from a mailbox of 2.3 GB. It did mention that some mail where skipped during the import process and I need to investigate that a bit more.
I’ve now restarted the export for the mailbox I’m experiencing problems with and we’ll have to wait and see if it goes better this time. The export process is ridiculously slow, it took 12 hours for the smallest mailbox and 20 hours for the largest. One interesting note is that after importing one of the mailboxes I temporarily got SSSD error as mentioned here, Account provider generic error: SSSD exit code 1. It disappeared after a while without I did anything about it. I assume it could be caused by too high load, my server has a i3-4150 and 16 GB RAM.
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