ummm idk if this sounds confusing, its hard for me to explain
you would make an new event on the boulder event, so event 1 (on the boulder) will have the sprite of the boulder, event 2 will be blank
in the NPC conversation have the boulder change to a blank sprite using the "Move event" tab then switch the event to the event with no boulder there
when u leave and come back the boulder should not be there