Leon and Castille separated and came back together (more than once) as a consequence of dynastic accident -- a king had more than one son who he wanted to inherit a kingdom, so the kingdoms were divided; later, one individual inherited both kingdoms and they came back together. Nothing was inevitable about either process; clearly it's possible for both royal lines to continue.
Conflict between the kingdoms was frequent but never decisive in OTL. It's possible, but not inevitable, for one to have conquered the other. It's also possible for either or both to have tried to get an edge by merging via dynastic marriages with the ruling houses of Portugal, Aragon or Navarre. Some combinations make more geographical sense than others, but that's never constrained anybody.