I was introduced to this book at the same time as The Elenium, in the early 2000s.
The sister had a large stutter at the beginning of the book. Brother is a lumberjack or something similar, has a lame knee and a finger that was cut and has healed with the excess skin folded over the nub. Sister's stutter came from an experience in some powerful magical area, a swamp of some sort? Happened before the events in the book.
At some point the brother went out for wood or work, sister is summoned via a horse to learn magic while brother searches for her. The sister's teacher is very old and she teaches the sister many things about magic. There is a temporal difference because while it takes the brother about a week to find her, she has been studying for years. This is evidenced by the loss of the sister's stutter.
The witch heals the brother's knee, says she can't heal the finger the same way but alluded that it could be done? The witch dies of old age shortly thereafter, and has the sister draw in her dying breath. This imparts the sister with a large amount of power.
The siblings don't go back to their cabin in the woods. Instead they go to a city.
UNKNOWN/HAZY aspects. Sister's magic is yellow? I think magic has color groupings. Sister has a friend. Maybe the friend also knows magic? Maybe the friend was also an apprentice to the witch (at the same time even?), or maybe they just met in the city.