Data about up-sells, cross-sells and related products in Magento is stored in catalog_product_link table. The link_type_id column specifies the relation between product_id and linked_product_id. Possible relations are:
1 – Related products
2 – Bundle products
3 – Grouped products
4 – Up-sell
5 – Cross-sell
So if you want to remove all up-sells for all products you can execute:
DELETE FROM catalog_product_link WHERE link_type_id = 4
Analogously you can remove all cross-sells and related products.
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