Ok, this worked:

- Backup the ~/.evolution folder.
- Export all the messages (after deleting duplicates) to a mbox format and 
import them.
   - For each folder, open folder, highlight all the messages and choose Save 
As.. to a file. This will create a mbox formatted file.
   - After exporting all the folders, delete the ~/.evolution folder.
   - Restart Evolution and import each of the files created before.

Thunderbird will have to wait :)

Mustali

-- 
evolution bug, "Summary and folder mismatch, even after a sync"
https://bugs.launchpad.net/bugs/27014
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