It shouldn't be possible to get rid of the Green Slab Key until you use it.
Try defeating the final boss again. Make sure to make a new save file when the game prompts. And then load up an older file, and the Green Slab Key should be in your inventory.
If it isn't, try visiting the Jungle Holding Site sub-locale. There's a locked door somewhere in that location that is opened by the key. Maybe you already have visited that place.