The issue is both BC(A1 and A2) and whey proteins(not part of the A1/A2 issue) are components of milk. The problem with A1 is not the intact A1 protein, it's the fact that it has a weak link in its protein chain and when this weak link is broken, it releases a peptide which is know as BCM7. This is the real devil in the milk which causes all the health effects for people.
Now, the breaking down of this A1 protein chain to release the BCM7 can be happen via digestion, but is also can happen through the heating and treating processes when processing and separating the milk components. So unless the the whey is derived from A1 free milk, then it may still contain the BCM7 protein fragments.
The savour of Australia's crippled dairy industry, page-13
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