What ended up working was the solution from nu2.nu. In summary:
- Move all mailbox files from the default storage location to another folder, leaving the default folder empty.
- Load Outlook, Import and choose "Import mail from on OE6 store directory".
- Select the folder from step (1) to import from.
The import process stalled on the Inbox folder for a few minutes, possibly resolving some issue in the process, then completed.
The export to Thunderbird then worked correctly.