There's always the chance that someone showed up at the airport with cash (well, credit card) in hand and was willing to buy an F seat, and if J inventory was gone, your friend was bumped all the way back into the class originally paid for.* I've been responsible for a similar situation a few times in 2014 - the agent at the desk even told me that I was going to make someone very unhappy as she issued my ticket and BP. As someone who upgrades a fair amount of time, I felt bad for the people who lost their upgrades, but at the same time I really needed to get to where I was going, the only inventory available at +2 for sale was F, so I did what I had to do.
*I have NO idea what the mechanics are to issue a BP in F when the original fare is Y and the upgrade is to J...would the inventory available for sale in F not have been reduced in this situation, allowing for someone to buy the seat even though it had been assigned?