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Regarding gwent

It used to be that anything that killed the strongest unit targeted any unit with the highest score even if it was a special card which cant be killed.

This effectively meant you could shield your cards from scorch (ect)
However if you used a commanders horn your normal cards would no longer be protected if their value moved above your special card value.

But since i started playing BOW it seams special cards are ignored for this purpose
No longer do i need to keep my normal cards value bellow my special card value for as long as possible to minimise the risk of a scorch

When did this change happen?
I think you are remembering wrong. I haven't noticed any change since release.