Problems in main menus and footer

Hello jaanthunez,
Not sure I get your issue.
This plugin just creates a basic child-theme for any (or most of them) themes. Also it has been tested mostly on Customizr and Customizr-Pro (it also has some special coding to better work with it). Anyways, it doesn’t “force” the inheritance of some options which *wordpress* itself handles per theme (like the menus).
A similar thing might happen with the widgets placed in the widget area.
You haven’t lost anything you just have to put again some “elements” in their position. But this is how *wordpress* works ??
About the menu, anyway, there’s a reference in the FAQs:
https://www.ads-software.com/plugins/childify-me/faq/

I created a child-theme but I lost my menu, how so?

Was that the problem?

Hope this helps ??