Hmm, it should be re-looping you for another 9 rooms before putting you back in the path to the pyramid core if you do that, although I did actually think about making a "Bad End" where choosing to spare the pyramid loops you in the maze forever, so that'd be neat too (but not intentional).
Thanks for playing!
EDIT: Oh, now I see. Sparing the Pyramid Core locks it out of its dialogue trigger, making it impossible to talk to it again. Oops! I'll push out an update that fixes it real quick (1.0b)