I'd try switching to the "advanced" role (resource bar -> roles -> content -> advanced). Save your current layout as a new role in case you want to switch back as you may lose all your current customizations, which sounds like it may not be a bad thing in this case.
You could use customize to put all the commands back where they started. Would it be easier to redo the previous customization or put each lost command back one by one?
Either strategy should get what you need; tedious work either way.
You can use MenuScript to customize menus, toolbars, and ribbons. The menuscript customizations are not as volatile as using "customize" and it lets you share the customizations site wide. It takes a bit more time to set up initially, but the benefits might outweigh the time cost.
Never heard about Menuscript before! I will take some time to look into that whenever possible. Thanks for the suggestion.
If you are going to research file based UI customization, I recommend this document: https://download.industrysoftware.automation.siemens.com/unigraphics/ugdoc/nx9/nx-9.0.0/NX_Ribbon-Cu...