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There is a CTX index on both the item and rev description columns. One of those should work unless the rev flags or item change are not set so you are not getting the latest rev in your search. You are close. It seems related to the data (load), not the index. Something is prohibiting the re-indexing from picking up the right data or finding it in the latest rev.
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There is a Smart Rule that is supposed to allow or disallow duplicate BOM entries. Are you saying that is already set to Disallow and you are still getting duplicate entries?
Averify can be run in different modes. One of which is to test for specific error types, (e.g. AGIL-00025135). Figure out the BOM error types you want to test for by looking at your previous reports. Then set in the config/averify.properties file.
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