If the file exists but just isn't loaded then you just need to load it. Open the Script Editor and go to the Popups menu (Alt+P), then go to File > Load in the menubar and point it at the correct popups.ini file.
Note that you'll have to do this once for each popups 'section' that's unloaded (ie. If your Status Window right-click is gone to you'll have to go to View > Status and load popups.ini for that section too).
