I know I'm late and I know the problem has been resolved... but part of being in business is the ability to control the situation as best as possible up front, and leave room for inevitable changes/occurrences should they happen.
I think you always have to take into consideration a change order/request, and the fact that it can happen at any time. In this case, yes I realize you've already put time, talent and money into the "present" design, but I think you should be flexible enough to allow some last minute changes. This example is what I would call a good change business speaking... in that you don't have to do anything new, in theory you've been paid for something which isn't needed. Not all change would be this easy and therefore would require more outlay of cash if there was time to complete the request.
You also have to walk a thin line between "professional judgment" and "fulfilling client requests". You might think the orange flowers were vital to the design, but I am a strong proponent of giving the customer what they want within reason. Maybe because I'm so exacting and know exactly what I want, I do so hate for someone to discount my thoughts and ideas especially when I'm paying for them to be done like I envision. I try to extend the same courtesy to my customers.
Now when someone has a death defying construction idea, and I'm uncomfortable with my ability to have the cake stand on its own, I'll politely decline the business. I recognize my ability. If someone wants a flavor I've never heard of, I offer to make them a sample to make sure their taste buds are agreeable to my way of making the special cake, their great aunt served them as a child... before I take on the order. This is my "professional judgment". When someone says they no longer want a certain color flower on their cake I would explain that I'll be happy to discard the flowers I've already made but understand those have been paid for already. It will cost X amount of dollars to fill that space with additional flowers and that is only if I have time to remake them. If I don't have time I would tell them that I'll be happy to discard those flowers, but there will be a void in the pattern as I have no time to create additional ones. In the latter case, time is finite and there just isn't time to do anything different.
I never get upset with someone over their change request - I just know what space of time I can and cannot operate in, and sometimes their money will dictate whether or not their change can occur. It is always their final decision. I'm not emotionally invested I guess you could say, in discarding something I've already done in the way of prep work. I always can use the practice.