From my experience, if your farrier is a professional (key word) and is knowledgeable of the job, he/she really shouldn't have any issues with you asking about questions on the trim. A good farrier will have your horse's welfare as their first priority and would not your horse to be uncomfortable.
Horses work 'out of' soft tissue problems. Sounds to me like you're flirting with a ligament, tendon or muscle problem. Just because it isn't as bad once she's warmed up doesn't mean there isn't something wrong....and the potential for something REALLY wrong. Changing angles drastically/suddenly is never a good idea.
Call the farrier. He might be able to take her heels down just a tad to make her more comfortable. Long story short: she may be out of regular work until her next appointment; given some time to grow.