Hi Gumbanomicon,
the error is most common when you reference a parent node that doesn't exist in the tree. Can you check your alchemy skill tree for missspelled parent nodes.
When you talk about hidden switches, do you mean the visibility requirements for tree nodes? Yes, you can use RPG Maker switches as requirements for the tree node to be fully visible. The switches need to be turned ON for the node to be visible. So your idea of turning ON switches once you've learned the node before will work perfectly.
Best regards,
Felski