Flying Club wrote back to me after I inquired about the ANA changes:
"Our codeshare agreement with All Nippon Airways is ending on 29 October 2016, however, we will continue our interline and frequent flyer relationship with them.
The fact our codeshare agreement is stopping will not affect your ability to redeem your ability to book flights on all routes with ANA using your Flying Club miles."
In practice though, I'm not seeing that.