A technique I used recently was to have my script write out two SQL files. One with all the fixes, and the other to revert everything back to how it was. The script took a long time to run but were completely non destructive. The SQL could actually then be examined and run on a copy of the database and the results checked, both the fixing SQL and the reversion (just check that both databases are the same again). Then just run the fix SQL on production.
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A technique I used recently was to have my script write out two SQL files. One with all the fixes, and the other to revert everything back to how it was. The script took a long time to run but were completely non destructive. The SQL could actually then be examined and run on a copy of the database and the results checked, both the fixing SQL and the reversion (just check that both databases are the same again). Then just run the fix SQL on production.