Normally counter shade sheds off but does it darken before shedding off? Along her spine its barely noticeable and she's shedding dark but get close to the hip its darker? The filly is a bay and is impossible to be dun. Posted via Mobile Device
What you're describing sounds to me like the hair that is growing in is dark, and she is shedding off the old hair. Horses don't shed then grow new hair, they grow the new hair in first then shed out the old hair.
If she is the foal in your avatar, then there is a good chance she is brown and not bay, in which case you can expect nearly every shed that you will be saying to yourself "what is going on this time".