Ah.... I thought you meant the query when it is looking for similar threads to put in the table. But, you are looking to do it when you are rebuilding them? Did you know you can start the rebuild in the middle? misc.php?do=updatethread&startat=xxxxx . xxxxx being the threadid to start at. Then it only builds those and the ones greater than that.
If you want to change that query to go backwards, it is in admincp/misc.php, look under do=updatethread and the query that select the threads is right there and it's ordered by threadid and the where statement is threadid >=startat .
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