Yes, anytime you update the the templates you’ll have to redo your custom changes.
Not sure when it’ll actually land, but I do have it on the drawing board to vastly improve the template API to support the overriding of the core template files. While this will provide the ability have update safe custom changes the downside will still be any new features implemented in the template could break the custom override or new features not being exposed because the file being overridden contains the code that implements/exposes the new feature. Of course I’m taking steps to mitigate that as much as possible but I’ll never be able to completely eliminate the possibility of the need for custom changes having to be redone after a template update.
Hope that makes sense!