Copay assistance question

Against instructions, CVS Specialty Pharmacy used copay assistance on file, rather than charging my credit card for an expensive medication. They admitted the error and corrected it - which means I’ve met my deductible. They also backdated this to the date of service, Jan 2. However, I had a couple of doctors appointments in the meantime, and even though my deductible had been met \*before\* these appointments - I now have pending charges that have not been paid yet. How do I handle this situation? Will my insurance reprocess these claims?