I am glad to hear that the issue has been resolved!
Here is my two cents anyway...
As a boarder, I believe that the owner of the horse has the right to dictate how they want to care for their horse, however if the owner is making decisions that will cause harm to their horse or the barn's reputation due to their ignorance you will unfortunately be held responsible. It is your property. If the SPCA or the sherrif was called, you would probably be the one who gets cited. Also...in this age of sue happy litigation, the owners of the horse could perhaps hold you responsible if something bad happens to the horse due to the animals poor condition, citing that as the professional, you did not steer them in the right direction. Probably wouldn't happen and it wouldn't be right if it did, but it is possible.
I think you should protect yourself by putting your suggestions in a formal, signed letter, along with the new feeding schedule or plan you agreed upon with the owners. Tell them that it is just to ensure you are both on the same page and you want to make sure they are satisfied and happy customers.
If you have problems with them in the future, maybe they are not the right fit for your barn. No harm, no fowl.