If your Cherry tree is badly affected by the canker, I would say it is best to remove it and burn it. It's hard to say if this will affect your new apple trees.

Agreed, but cankers on old trees MAY not affect new healthy stock. Like us, old uns suffer from more than young uns! I would give the apple trees (on certified clean stock) a go. Worthy

Thanks for your replies. Think I will try with the new trees.