Magento stored all Data about up-sells, cross-sells and related products 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 Related products for all products you can execute:
DELETE FROM catalog_product_link WHERE link_type_id = 1
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