This thread is resolved. Here is a description of the problem and solution.
Problem: Does the Custom XML Configuration get lost during plugin or theme updates?
Solution: No, that data is stored in the database and not overwritten during updates to the theme or plugins.
Relevant Documentation: https://wpml.org/documentation/support/language-configuration-files/
This is the technical support forum for WPML - the multilingual WordPress plugin.
This topic is split from https://wpml.org/forums/topic/translated-pages-dont-appear-in-the-front-end/