EDIT: I'm using version 2.79b and Cycles Render.
I have motion capture data for a number of markers that come from a suit in a VICON MoCap studio. I also have a number of animations of the same subject. When I import the c3d data file, the markers are all imported as objects within the space. These move as the timeline is played.
To manipulate my character mesh, I have it parented to an armature with weights painted accordingly. I then have parented the armature to the C7 spinal marker. This allows it to follow the "root" marker through space. All of the other bones have damped track bone constraints to their relevant markers to allow them to follow the markers through space.
To record the animations, I'm inserting keyframes (LocRot) using the action editor and then pushing actions to the NLA editor. After saving these, I need to import a new animation (say, "jog" comes after "walk"). All of the markers are labelled the same. So my solution is to delete the current markers before starting again. A long process, but fairly quick once comfortable. The issue I have is that any saved animations are not staying the same after the markers are being deleted or even if I remove the bone constraints. If I remove these, shouldn't the bone keyframes still stay the same?
I can't figure out how to keep the bones from "forgetting" where they were during a keyframe. Am I misunderstanding how it works? Are there any solutions that I am not considering?