Check out this video: http://www.youtube.com/watch?v=m2eecggyVr0 on replacing drums with audiosnap. Bounce the clips to one clip. use audiosnap to create midi from the clip, use your favorite VSTi to trigger whatever kick drum sound you would like to use. There may not be a simple copy / paste solution but the work around isn't bad if this is something you really want to do.

Rocky

You can drag and drop an audio sample kick into Session Drummer.  Then you can just copy your kicks to a new midi track, triggered by the session drummer kick (with your audio sample loaded)

Or you can render your midi kick track to audio.  Show transients.  Then insert a new track under your old midi kick.  Tab to each transient in the midi kick track, and paste in the new audio kick at every transient, this way lines up with the previous kick.

Heres a quick sample I thru together - hard to hear but ya get the point

As far as a sample you like, its just a matter of selecting the sample you want thru SD3

http://www.youtube.com/watch?v=OHPDQCtYE2Q

Perhaps not terribly elegant, but I have used a quick and dirty trick for this sort of thing before.
Temporarily rename the file.
Change Kick1.wav to something else, like Kick1Holding.wav.
Rename Kick2.wav to Kick1.wav.

This works because the clip itself is not actually in your track. The track just contains markers telling Sonar to play Kick1.wav at X point in time.

Play the track to make sure it sounds right.
Bounce the track, and you're done.
Don't forget to change the file names back to their original state.