Transmission problem
1998 Audi A6 6 cyl All Wheel Drive Automatic 90,000 miles
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I had a complete brake job done, when the car was driven less than 10 miles the right rear break locked up to the point that there was smoke coming from that area.

My question is, could this have caused my transmission to fail after driving less than 50 miles after we got it back.
The transmission drops out of the top gear and goes one gear down.

Pendulum shifting (that's the technical term) could be caused by several things and might be related to the mishap with the brakes, yes.