That is what we do except that we use dummies instead of bones.
The object I'm trying to animate is a pendulum that goes down on its wire every once in a while. We have a main looping animation where the weight goes left and right, and several non-lopping animations where it goes down a few centimetres. The effect I'm trying to achieve is to have the pendulum go down at any point of its oscillating cycle.
We're using dummies and not bones because we want them to be animated independantly, and bones always have some sort of IK chain. But we tried bones anyway and it didn't seem to change anything: the main animation plays, but not the channelled ones...
We just put "buffer" dummies to the hierachy to make sure that no dummies influenced their neighbours, but it doesn't change anything. We also made a special animation with just frame 0 to be extra extra sure that no keyframes are shared by the animations but it still doesn't work.
Any ideas ? Or maybe there is a better way to to what I want ?