Even with the full panel, deletion mutations often aren't tested for, so there is still a gap. I was tested with the full panel and had an unidentified mutation when I was younger, but it was later discovered that I have a complete deletion of the CFTR gene on one side. My sweat test numbers weren't borderline though, so I was able to be "diagnosed" even without knowing my second mutation.
Ask your CF doc (or whoever ran the Ambry panel) whether the test checked for ALL KNOWN CF mutations including deletions. If the answer is no or even "I'm not sure", demand more answers and possibly more testing. Believe me, all the trouble will seem more than worth it if it turns out your child needs care that she is not currently getting because of a botched diagnosis.
Good luck, and I also want to add my congrats on clearly being a very persistent parent. Whatever is causing your daughter's medical issues, she is lucky to have a mom with the drive to get her the care she needs!