Hello,I'm usually a lurker and can't become a member until I get a computer of my own, but I couldn't resist this thread so here are my 2 cents.
I too was a classical flute player for many years. I had to stop playing not long after high school because of severe tendonitis and an inflammatory muscular disorder. But, before I quit I went through a while of being very careful: here is what I learned.
1)Sit up straight (this means neck, shoulders, hips etc are in alignment). 2)Keep shoulders down and even. 3)Stretch your neck, shoulders, arms, wrists and fingers before beginning to play 4)Sit on the edge of your chair: NEVER lean back. 5)Avoid hard angles for your fingers and wrists. 6)Don't tense fingers or wrists **(actually there is a way to mostly use the larger muscles of your upper arm when playing instead of the smaller muscles of your wrists and fingers)
You may want to see an occupational therapist. There are some who specialize in treating injuries common among musicians.
Cheers, Leila