Answer
Unfortunately this known issue won't be fixable soon. In the meantime, follow these steps to workaround it.
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In the Custom Field Sets tab, select the Custom Field Set you want.
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You'll notice that there are two save buttons. You will need to upper one to save changes specific to custom field sets first.
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You will then be able to use the lower save button to save the entire Product.
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If this appears not to work- wait a few moments and refresh the Page. It can sometimes take time to build the Custom Field Set as a model in the Database.