[Johnjy]

I found an issue involving the Favourites script, the Backup add-on and at least the Xonfluence skin (if not other skins). I found a work around, which I thought I should contribute in case other's have the same issue. This occurred with Kodi 19.3. The Kodi log did not record anything relevant, but the issue is easy to reproduce (in fact, it was impossible for me to avoid).

Issue: after backing-up/restoring an installation using the Kodi Backup addon, it is no longer possible to select favourites to program the behavior of Home menu items, addon shortcuts and submenu items. When you try, as soon as you select "Selected Favourites" you are returned to the settings screen and don't have a chance to select a favourite. FWIW, this is the same behavior you would experience if the favourites list is empty.

Work-around:
1) After restoring from backup, disable the favourites script from running. In the Xonfluence skin, this setting can be found in System (also called settings in other skins)\System\Skin Settings\Scripts Options\Supported Addons and scripts\Enable favourites script.
2) Uninstall the favourites script addon. This confused me because I couldn't find it in the add-on browser. You'll find it in System (also called settings in other skins)\System\Add-ons\Manage dependencies
3) Restart Kodi
4) Re-enable the skin's Favourites Script support, this should trigger the download and re-installation of the Favourites Script addon
5) Restart Kodi

It is possible that one or two of these steps are unnecessary, but this is what worked for me, so I thought I'd report my process faithfully.
I hope this helps someone.