If I disable popups, my custom settings, using "A Custom Attribute Display" option, are deleted. There are legitimate reasons why I want to disable popups from time to time. Resetting the custom config creates a lot of extra work, and seems like an unintentional bug.
I don't have a solution for you but I feel your pain. Maybe you use this workaround. I have each custom popup saved as a text file so that I can quickly paste them back in if the pop ups get disabled.
That's a great idea. I did something similar to reuse some complex (for me) code for another project. I'll just create a list of custom popups until this is fixed or improved.
I would recommend you checkout this workflow in Map Viewer Beta. This is something we added support for preserving the popup after you disable it.