try lassoing the clip.
I know exactly what your talking about. cake already knows about it and hopefully we will see this fixed.
but for now its easy enough to either hi-lite the track and bounce to clips or lasso the clips, (right click/drag)
then bounce them to clips.
I get in the habit of keeping clean tracks, meaning every few edits or so I double double click the tracks selection button(this sometimes can hi-lite everything) so then click the selection button once more and now everything in your track should be a lighter color (meaning all data in the track is selected)
now bounce to clips.
if you want to do just small sections use the lasso method as explained by me earlier, just as to make sure you lasso from both edges, one side of the clip to the other, if you don't you may miss a piece of a clip underneath.
now all your clips are on one layer.
good luck hendrikxix