BTW, you posted in the Lion forum instead of Yosemite. For best results post in Yosemite the next time.
We need to determine if this is a Spotlight issue or a problem in Mail. It would be helpful to know what type IMAP? iCloud, Gmail, Yahoo, Outlook.com or other.
If you search in Spotlight in the Finder (top right in menu bar) for the message subject does it show up? If yes, can you find the message in Mail search?
HOW TO RE-INDEX YOUR SPOTLIGHT CACHE FILES
Option 1)
From the Apple menu, choose System Preferences.
* Click Spotlight.
* Make sure Mail & Messages is checked under the Search Results tab.
* Click the Privacy tab.
* Drag your drive to the list. Wait a couple of minutes.
* Remove the item you added.
* Spotlight will re-index the contents of the item you initially dragged to the list.
Option 2)
Follow the steps here.
Use OS X Recovery Disk Assistant to reset Your files and folder permissions
When you restart Spotlight will reindex your entire drive.
Option 3)
Copy the text below and open Terminal (in /Application/Utilities). Paste the code into the Terminal window at the prompt.
sudo mdutil -E /
You will be asked for your administrator password (and if you've never used the sudo command you'll need to accept the warning presented). When you type your password, it will look like nothing is being typed. That's normal. Once you've typed your administrator password, press Return.
This will completely remove the Spotlight index and force a new one to be created. Probably not necessary, but I would immediately quit Terminal and restart your Mac.
SUMMARY:
Depending on your Mac and the contents of it's hard disk, re-indexing may take several hours. Doing this overnight is a good option if you have a large drive.
You can tell if it's still in progress by simply looking at the Spotlight menu: There's a blinking dot in the middle of the magnifying glass while indexing is occurring. You can also open Activity Monitor in Applications/Utilities and type in md in the search filter. You should see mdworker32 and mdworker. mdworker32 is the Microsoft Outlook Spotlight index and mdworker is for system.
Until this process is finished, Spotlight won’t know the contents of your disks and neither will Mail.
