Both quotes of the manual are correct, but the first should mention that spell craft skills are not as effective anymore, even though you can still train them normally. It is right for all other skills and traits.
Learning spells has two constraints: you can't learn spells higher than your spell skill level AND you can't learn spells higher than your current role level. The second constraint is always true, not only after class change, but you won't notice normally because your spell skill will mostly be lower or equal to your role level. So conflict: no, confusion: yes.
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