For those suffering from this problem:  A working workaround.

1. Set Evolution to Offline mode, exit evolution

2. Open terminal and run  evolution --force-shutdown

3. find ~/.evolution/mail/local/ -name \*ev-summary -delete

4. Re-start Evolution.

Warning: this involves automated file removal which can result in data
loss if done incorrectly.  I take no responsibilities. Read "man find"
to understand what you're doing.

Step 2 is *essential*.

To avoid further corruption of your Evo folders: Always put it in
offline mode before exiting.  This avoids the mailcheck ruining the ev-
summary files while the folders are being loaded and works around the
bug on my system.

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