I can confirm that the 10.3.1 update does, in fact, prevent the Mojo from working with the iPhone SE and Apple's own Lightning to USB Camera Adapter. It would be helpful if users with this issue could state the which model iPhone or iPad and Lightning cable they are using. This will help other readers determine which devices are and are not affected.
Apple needs to be slammed for issuing updates that were not fully tested and prevent peripherals from working with the Lightning port. Given that Apple made the decision to eliminate ports and force manufacturers, app developers, and customers to use Lightning and USB Type-C adapters, they in turn must do a better job testing updates.
These reckless updates will severely hurt the third party manufacturers who spent billions of dollars across various industries to develop and produce devices to work with the Lightning cable. Your post is one of many I have read tonight from customers that are losing confidence in the devices they purchased or plan to purchase-- and I feel the same way. I imagine for a business owner like John Franks it is especially frustrating knowing Apple has instantly rendered his products useless for many owners.