If you change the bounty chip cost, the software will look through the buy-ins and determine if anyone purchased a bounty chip for a different cost (different than the amount you've just changed it to). If so, the software will ask if you want to change all previously purchased bounty chip costs to the new amount.
This makes it easy to correct a mistake - the mistake being you set the bounty chip cost to the wrong amount. This only changes the cost of already purchased bounty chips. If a player didn't buy a bounty chip (indicated by his/her bounty chip cost being $0), it is not affected.
Unfortunately for you, it sounds as if you didn't set a bounty chip cost, so changing the bounty chip cost amount won't help [because no one bought a bounty chip]. You can still fix your tournaments, it just won't be as easy.
To fix, you'll need to edit each player individually (on the Players tab). Double-click a player to edit. On the Edit Player dialog, in the Tournament History section, double-click the first entry ("Initial buy-in") and change the bounty amount. Do this for every player who bought a bounty chip.