I know this is not the solution but it is a work around that works!

Please make sure you back up the relevan data file for the problem
folder first, just in case.

Often when the mismatch message occurs evolution cannot generate a .ev-
summary file, especially with large (500+ Meg) files.

To overcome the problem for folder FOO

Make a new folder FOO1

go to FOO and select all emails

Move all mails from FOO to FOO1

select FOO1 (the mismatch error will come up again as you leave FOO)

Check all the mails are there.

Quit and restart evolution to check the data is there, select FOO1.
Then select another folder to make sure the error does not occur on this
new file.

Delete FOO (you need to expunge it first)

Rename FOO1 to FOO

Everything should now work.

Finally, for good housekeeping check the
~/.evolution/mail/local/Inbox.sbd/....... directory to see that the new
files are all listed as FOO.

This does not always happen (some will retain the FOO1 element) and it
will not cause a problem but will be confusing if you regularly check
the evolution directory and file structure so;

Instead of renaming FOO1 to FOO

Stop then restart evolution

Make a new folder FOO

Move the files from FOO1 to FOO

Stop start and check once more

Delete FOO1

Hope this of use to beleaguered evo users

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

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