Huh, interesting. Unfortunately, I don't have any devices with Safari so I can't try to replicate this myself. A few questions to try to figure this out: Did you run into the same issue with Chrome? Was this on a mobile device or a computer? And, just to make sure I have a clear image of what you're describing, when you say it disappeared, does that mean that the menu links would appear in the footer but when you tried to click on them the entire bottom menu would go away (and freeze the game) or was it even just hovering over it or clicking on it in general that would cause it to disappear?
This was on the Safari browser on MacOS on a desktop computer. When I switched to Firefox on Mac the problem stopped...so you might just want to note that Safari may not be supported.
Once into the game with the lower menu (I think it had options like "Me - Them - Facts" ?) attempting to click on one of the lower menu options made the words seem to 'race off the side' like it was an animation that played wrong and the words disappear. This caused nothing onscreen to be clickable further until the browser page was refreshed. The game would load again, links in the story were clickable but if the menu is clicked the glitch repeats.