This is a very good question, and one thing we had issues with over the years while developing EteSync. At EteSync, we ended up building client side debug utils that we can get users to launch in order to figure out what's going on and selectively report issues. You can, depending on your users' risk profile, also have it more automatic (we kept it semi-automatic).
Developer tooling is definitely lacking at the moment for building encrypted applications and it's something we plan on addressing.
