I should start out by saying that I'm not sure about any of this, so you'd be trying it at your own risk and you should have a database backup if you don't already.
Anyway, in the admincp under Maintenance > Update Counters, in the Rebuild Search Index section, there's a link to remove the indexes. Of course after you do that no one will be able to search until you rebuild them (assuming it's a live site you're working on - if not it of course it won't matter).
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