Q: On a MacBook Pro I was using a USB footpedal to start and stop audio transcriptions. When I upgraded to El Capitan, the  pedal does not work.  Will Apple remedy the situation?

No. You need to contact the makers of the pedal.

Just got off the phone with Olympus (my foot pedal maker).  They don't have a fix for this yet.  They did advise NOT to uninstall the olympus software and try to reinstall as it will NOT let it reinstall and will cause more issues.  To just wait until there's a fix, could be 3 weeks, or to use an older computer without the El Capitan update or a windows computer as if i owned one. 

UPDATE *****

Contacted Apple and they are helping me revert to previous OS by restoring from backup.  Just FYI that there is another option other than just waiting.