@billyudi We are working on a update to the upgrade guide which will discuss how to map the new theme files and changes.
You can follow along with it here:
https://github.com/FusionAuth/fusionauth-site/pull/2166
I get your larger question though, which is, if I customize my theme, and then I upgrade from 1.45 to 1.46 and 1.46 introduces a new themed page, what does that new themed page look like?
Have you tried testing this out?