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Does the Shopify 100 variant limit come into play?

It could or it couldn't. Basically this app will double the variants on a product so as long as you have 50 or less already you will be fine. If you have more than 50 variants on a product it will not be able to use that product in a bundle sale. There's nothing we can do about that, Shopify has a 100 variant limit on products.
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