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UPDATE: A lot of people have brought up how easter eggs are scattered throughout all the Pixar movies. They transport across time and that is why Merida couldn’t find the witch.
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You remember Merida opening doors and the witch constantly disappearing? It’s because those doors are made the same way from Monsters Inc. If you look closely, you can see the carved truck below. We even see the Pizza Planet truck carved as a wooden toy in her shop, which makes no sense unless she’s seen one before (and I’m sure she has since that truck is in literally every Pixar movie). How do we know? In Brave, you can briefly see a drawing in the workshop.
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She probably went back in time to the Dark Ages to get more magic from the will-o-wisps. UPDATE: Just to clarify: The theory is that Boo discovered a way to use doors to travel through time on her own, possibly by developing magic on her own. They are what started everything, and as a witch, she cultivates this magic in an attempt to find Sully by creating doors going backwards and forwards in time. She figures out how to travel in time to find Sully, and goes back to the source: the will-of-the-wisps.
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