AudioSnap Phase Issues

After much experimentation I think I'm getting the hang of AudioSnap. I'm trying to fix the odd timing issue with a 13 track drum recording.
I've used the snare and kick drum track to provide transient information. So far so good, I'm able to move the transient markers around and the whole 13 tracks are time stretched accordingly, due to my markers being merged.
 
However, upon bouncing to clips, I'm getting phase issues. I'm not making huge changes either.
 
I'm not at my DAW right now but have been thinking about this. I have 2 mics on the kick drum - beater and head and it's the kick drum track that's suffering a noticeable "thinness" due to phase after bouncing down for the stretched sections.
 
Am I correct in thinking I'll have to use the transients from both kick mics and move these together to get phase accuracy on the kick?
 
Thanks,
 
Mike.