I have had several unfortunate experiences with Evolution in the last 12 months or so. Lost mail, lost folders - all of them !!!.
The mail still existed, and in one case mail was still being fetched, but not appearing (as no folders), but was on disk.
All (evolution) recover efforts failed. I have now migrated all my machines to claws. It was able to import mail folders (on disk) that evolution couldn't even find. Go figure.
Maybe not much help to you, but I know what you're experiencing.