OS X’s Mail program has a built-in way to help resolve issues with garbled messages or with emails not appearing when you search for them. This option is available under the Mailbox menu—it’s at the bottom, labeled “Rebuild.”
If you pick any mailbox from the sidebar and then choose that, Mail will attempt to, well, rebuild the mailbox, which can help with all sorts of display problems and emails that seem to be missing.
Note that if the mailbox in question has a ton of messages, this process can take a while. You can monitor the progress by choosing Window > Activity from the menus at the top.
And one more thing, as Apple notes in their support article on the topic:
When you rebuild mailboxes for IMAP or Exchange accounts, messages and attachments stored on your computer are discarded, and then downloaded again from the mail server to your Mac. Your mailbox appears empty until the download is complete.
I’ve also found that you may have to select a different mailbox and then click back on the one that’s rebuilt to see that mailbox’s content after the process is complete, or you can quit Mail and reopen it to do the same thing. But after that, you should see a new and improved version of the misbehaving mailbox. If the issue still isn’t resolved, though, be sure to check out my tip from 2014 on solving Mail searching problems. You’ll have to adjust the steps a bit if you’re running a newer version of the operating system, though; where I give the path as “~/Library/Mail/V2/MailData” toward the end of the article, you’ll want to change that to “~/Library/Mail/V3/MailData.” Silly Apple, changing things up and making my old tips obsolete.