I have been having some weird problems on my new retina MacBook Pro with Mountain Lion 10.8.2.
First, Time Machine backups slowed way down and eventually quit working, then my email started being unsearchable, and finally Spotlight itself appeared to simply quit working.
After much investigation, I believe that not only did Spotlight corrupt the search index, it also corrupted Apple Mail and Time Machine. I had to fix ALL THREE to make things work right again. I went through several steps to rectify this, which I thought I would document here.
Here is what I did to fix the issue for me.
First, in Apple Mail I did the following (hat tip to Glenn Leblanc for this tip, posted here: https://discussions.apple.com/thread/3888378?start=0&tstart=0 )
Quit Mail.
Go to the Home Library folder. This is hidden in Lion. To get to it, select GO in the Finder menu while holding the option key down. Select Library in the submenu. Then navigate to Mail folder/ V2 Folder/ MailData folder. Find the Envelope Index Files. Move just those files to the desktop or trash and restart Mail. Select continue in the message box that comes up. The rebuild could take a while depending on how many messages you have.
This resulted in being able to search for contacts, and subjects again in Mail, but whole message searches (body text) still did not work.
Then, I tried to force Spotlight to reindex by following the traditional route:
System Prefs > Spotlight > Privacy Tab
Add your startup hard drive to the “prevent Spotlight from searching these locations” list (use the “+” symbol at bottom)
Close and reopen System Prefs
Remove your startup hard drive from the same list using the adjacent “-“ symbol
This did NOT work for me. When I would check the Spotlight popup from the right side of the main top menu bar, no indexing activity was shown.
Then, I tried a Terminal command to force reindexing (Applications folder > Utilities Folder > Terminal app) as documented here:
http://jonathansblog.co.uk/how-to-force-spotlight-to-reindex
sudo mdutil -E /
I got back a cryptic message that stated “indexing is disabled” (this would account for why I was still unable to do context search of mail messages)
I found this link and implemented “Solution 2” using another terminal command to re-enable indexing:
sudo mdutil -i on /
This started Spotlight indexing again, which was verified by checking the Spotlight search box on the main menu bar again, and seeing the “thermometer bar” indicating indexing in progress.
After the indexing was completed, I formatted the Time Machine external backup hard disk drive, and started a new Time Machine backup. The backup performed a 40 GB backup via USB 3 in less than one hour.
It appears that I am now back up and running, able to search Apple Mail, do normal backups, and use Spotlight in the Finder. I hope it stays fixed! I will post any updates, good or bad, here.
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Update 11/5/2012
Time Machine bogged down again, slowed to a crawl. I read another tip on how to fix this issue via posts by others folks here:
https://discussions.apple.com/message/19316035#19316035
This is another terminal command and can be summarized as follows:
How to run tmdiagnose
1) Launch Terminal.app (/Applications/Utilities/Terminal.app)
2) Enter the command text below followed by the Return key on the Terminal command line:
sudo tmdiagnose
3) Enter your admin password when prompted and wait for all of the tmdiagnose processes to finish.
I did this, and then hooked up my backup drive and ran Time Machine - it backed up 3 GB in a few minutes over my USB 3.0 connection.
Hope it stays fixed this time!
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Update 1/7/2013
Still broken! :( Time Machine will work for a time or two and then go back to it' old slow sluggish, freezing self. Not happy. This has been going on for months with no fix from Apple. I am trying a tmdiagnose, as described above, to see if I can get it to work even temporarily again.