Missing or even misbehaving elements from the InDesign interface can often be brought back by deleting your InDesign cache files (which is not the same as deleting preferences). Hopefully, this will make your reference point icon fully functional again.
To do so on a Mac:
The User Library folder in which InDesign’s cache files are stored is hidden by default on most Macintoshes. To access it make sure that InDesign is closed and click on the desktop to launch a Finder Window (Command-N). With this window in column view follow the path User>Home folder (it’s the folder with an icon that looks like a house—it may have the user’s name rather than “Home”) and click on the Home folder. With the Option Key pressed choose Library from the Finder Go Menu. “Library” will now appear within the Home folder. Within the Library folder find the “Caches” folder. Within the Caches folder find and delete the entire folder “Adobe InDesign”. I find that deleting the InDesign cache folder completely leads to a lasting change.