'Your Mail index has been damaged.'
'Your Mail index has been damaged. To repair it quit Mail. Mail will repair the index the next time you open Mail.' Have done it several times but just get the same message.
iMac, OS X Yosemite (10.10)
Send Apple feedback. They won't answer, but at least will know there is a problem. If enough people send feedback, it may get the problem solved sooner.
Mail/Provide Mail Feedback