Technically, every power of every class in Eora is fueled by their soul, and if a god sapped the strength of your soul it would be the equivalent to a level drain. It has nothing to do with knowledge. This lore was indeed laid down in the beginning of Pillars of Eternity's original kickstarter campaign.
I'm not saying it makes the writing good, or 100% realistic, but it makes sense based on the setting and its lore.
I'm not sure I buy that for, say, your skill point allocation or basic combat training. Those shouldn't just vanish unless something more fundamental happened, like your entire form is reconstituted and soul re-attached to the new body. On the other hand, it should give your character a powerful motivation to track down the root cause and get his or her experiences back. Or at least to think that is what they are trying to do.
Maybe later on you will meet your true form, and find out you were soul-cloned?