The problem may occur when you switch between themes in Appearance -> Themes is that widgets may lose their positions. It is a WordPress behavior and we are not able to fix this in our theme scope. Now, you need to go to Appearance -> Widgets and move all widgets to appropriate positions.
As a workaround, you can backup your widgets configurations using this plugin https://wordpress.org/plugins/widget-importer-exporter/
We don’t know how exactly you customized template files so we can’t answer is it serious or not. It is not our theme problem or a bug but just a notice that you customized template files from old WooCommerce version and they are already updated.