Blender Underground

How to disconnect/deattach bones from each other and still keep the animations intact?

I'm working on a model format which stores bones relative to root (0,0,0). There is no parenting info.

However, my importer allows to connect and parent bones during import, so the models can easily be posed and animated.
The exporter in it's turn disconnects the connected bones before export.

The problem is if I create animations for the model when the bones are connected, then the animations will mess up when I'll disconnect the bones. That sucks a lot. I thought maybe there's a way to tell Blender to apply the transforms to child bones as well, so when I'll disconnect them, they will move as well and not stay in the same place.