I've always avoided windfall fruit for anything other than animal feed due to the fact that at the very least, it's bruised & at the worst it's harbouring nasty bacteria/yeasts/molds/etc... Find out more about cedar-apple rust here
Cedar-apple Rust As far as how cedar rust will effect cider: Rusts are fungi, like a mushroom, or the blue/grey fuzzy stuff you see on old bread. In all honesty I cannot say for certain that it will, or will not have an effect on your cider; BUT, that having been said, do you really want to introduce a fungus into something you're going to be drinking? I wouldn't think it would be able to survive in the bottle, but you never know. If you're intent on using the "good fruit" from an infected tree, I would think sanitizing your fruit (whole) would kill off most, if not all of it. And I would still sanitize the must before pitching your yeast. I wouldn't use any fruit that had lesions though. You might consider spraying with a fungicide at the appropriate time of year to rid your trees of it. Sorry I couldn't answer your question directly, but I hope this "indirect" info will be of use to you. Regards, GF.
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