As you may know, the substitution levels, as introduced in Champions of Valor are, as quoted:
Substitution levels are levels of a given class that you take to gain certain benefits instead of the level benefits associated with the standard class. Selecting a substitution level is not the same as multiclassing; you remain in the class for which the substitution level was taken. The class features of the substitution level simply replace those of the normal level.
My question is what happens to the level-based benefits of an ability that has not been replaced at the substitution level? Spellcasting is explicitly described as "unless stated" spellcasting is increased. I'm referring to other abilities, let me give an example to elaborate:
-- Paladin 6 vs Paladin 4/Crescent Moon Knight 2 (who has taken both 4th and 6th levels)
How much does Lay on Hands heal for the 2nd character, with a Cha score 12?
6 or 4?