You could try truncating those catalog_product_flat_* tables. Backup your database and then via MySQL console, phpMyAdmin or other MySQL client run the following:
truncate table catalog_product_flat_1; truncate table catalog_product_flat_2; truncate table catalog_product_flat_3;
Do this for all catalog_product_flat_* tables. Then re-index the Product flat data index to rebuild / repopulate those tables.
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