Any runner who is over fair territory and is struck by a batted ball prior to passing a fielder is out, there is no protection by being in contact with the bag. There are a few exceptions to note: 1) There is an infield fly and the runner is in contact with the bag when struck with the batted ball - Ball is dead, Batter is out and runner is safe. 2) Ball is deflected by a fielder and no other fielder can make a play on the ball - ball is live and runner is not out.
There are a couple more that I would need to think about, however, in your sitch, if the umpire felt that ball was over foul territory when it struck the runner, it is just a foul ball.
Hope this helps.
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