I do think whats going on with thoughts and feelings is important too.I do increase her food periodically but I believe her emotions burn this up or prevent absorption. So it really comes back to having the correct thoughts so that the food benefits.
But calories are calories, and if she is needing to grow and heal, she may need more than you think. I think member @Jennifer had a patch of eating several thousand cals a day for a while during recovery (similar height to your sister, needed to rebuild a weakened skeleton).
Or could also be something she's having trouble digesting that she's not getting what she needs from? Some personal intolerance, or - and I'm not well informed in this area, just thinking it could be another avenue to consider if you are running out of ideas - trouble producing the digestive substances. I know some people here say they've had benefit from either betaine HCL or digestive enzymes - you could search out those stories.