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Yes, if you scan your Flybuys at participating retailers as you normally would. If you then pay with Flybuys Dollars in-store at a participating retailer, you will earn points on all eligible purchases (assuming no bonus points offers are applied).
For example, if your total is $50 and you have used $40 Flybuys Dollars, you will receive points on the full $50 (assuming no bonus points offers are applied).