So I digged into the source and found a makeshift solution to this problem. The problem is that during the creation of the new DerivedMesh, the CustomData layers are created as empty, but not copied from the original dm. A makeshift solution for just the freestyle edge mark is below (using the fact that the original splitted edges are at the end of the new table). I hope this helps, but I think this needs a more general solution.

source/blender/blenkernel/intern/subsurf_ccg.c
L3752+
...
ccgdm->dm.numVertData = vertNum;
ccgdm->dm.numEdgeData = edgeNum;
ccgdm->dm.numTessFaceData = faceNum;
ccgdm->dm.numLoopData = loopindex2;
ccgdm->dm.numPolyData = faceNum;

/* add new code from here */

#ifdef WITH_FREESTYLE

       	{
		FreestyleEdge *dstFed= DM_get_edge_data_layer(&ccgdm->dm,CD_FREESTYLE_EDGE);
		FreestyleEdge *srcFed= DM_get_edge_data_layer(dm,CD_FREESTYLE_EDGE);

		if (dstFed && srcFed) {
			int	max= edgeNum - totedge * (edgeSize - 1);
			int	i;

			for(index= 0; index < totedge; index++) {
				   i= max;
				   max += (edgeSize - 1);

				   for(; i < max; i++)
				   	dstFed[i]= srcFed[index];
			}
		}

}
#endif

/* new code end */

/* All tessellated CD layers were updated! */
ccgdm->dm.dirty &= ~DM_DIRTY_TESS_CDLAYERS;