Yeah, don't they have any signs up with "under new management" or any other notices like that?
If this lady was a long-standing customer, though, give her a refund and making a note that when she orders cakes she'd prefer to have the thinner layers isn't a big deal. Just knowing that she's going to be a special order customer will let you do the cake the way she wants them in the future. Charge her extra if you need to, but if you're going to do that then THE OWNER needs to talk to her and give her the option of having the three layers or paying more for six.
I have to add that you seem to post a lot, and it's usually about second-guessing the owner's decisions. Are you just trying to learn how other people would handle situations that arise, or do you spend a lot of time arguing with the owner about this kind of stuff? I remember that you explained what your position was at the bakery before, but I don't remember if you're an assistant mananger or what. I'm just curious, because you said that you do take your job seriously and have been given a raise, so that's good.