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Is it possible to reindex flat product and category tables without having them enabled? I need to enable them but it hasn't been done in 2 years so don't want to leave a live site for 20 mins+ with products and data from 2015!
Have you tried to reindex through the command line?
For example Flat Category:
php shell/indexer.php --reindex catalog_category_flat
And for Flat Product:
php shell/indexer.php --reindex catalog_product_flat
Required, but never shown