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Association type of 'Replace' causes the product to be replaced both in Sales and Purchasing.

Workaround if you need to order stock for a product with an association type of Replace.  Go to the product>associated products>change the association for a second to cross-sell and save. Then place the product onto a manual purchase order remembering to set the product back to the original association type of Replace after saving your purchase order.
However, you can also create a purchase run for that supplier and manually add that product to the purchase run line without making any changes to the association type.