The modification you made from the main system where you define new code lines for copying or removing selected values under the combo_lists is certainly in contradiction with specific code lines from Dynamics CRM Deployment logic, and this could explain that maybe your main system allow you this functional modification. But when you face mobile devices syncing technology thru your main sytstem, users cannot use your additionnal commands because their technology is evolved thru Apple or Android, mainly, and the specific javascript command you have self implanted do not define CRM logical accessing and syncing thru native commands specified by mobile devices.
In other words, if you want to allow mobile devices to have access to your add in, this modification should be available to all devices synchronizing with your business_system.
Happy modifications...!!!