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Have you rebooted, and if so does this reindexing continue? Have you tried killing the process from the Activity Monitor (in your Utilities folder)?

I would suggest e-mailing Omni via the Help->Send Feedback command in OmniOutliner. You'll get a response from them pretty quickly.

If this continues after rebooting you may also want to post on the Apple support forums to see if there is something that they can suggest.

James B.