I just had this issue happen on two songs. I had manually edited the transient markers on my kick drum track, created MIDI notes, and pasted them into a new MIDI track. Then I went to edit the transient markers on the snare track and it didn't show any active markers. I could see the disabled markers for the mic bleed on the track, but the big snare hit waveforms had no makers for the whole song. I had previously edited markers on this track as I already have a MIDI track for it. I was just going in for one last fine tuning pass on transient marker position.
 
Does anyone know what causes this and how to fix it? Note that I successfully edited a couple other songs between the two songs that are giving me trouble, so it's probably some project/track specific setting that got hosed up. Fiddling with the threshold slider will enable the markers on the small hits, but not the big ones. Weird. I'm a newb at this AudioSnap feature so pardon my ignorance how it works under the hood...

I don't what caused the issue but I think I have found a way around it...
 
If I select all clips that have AudioSnap audio (Edit | Select | All AudioSnap Clips), then disable AudioSnap on all the clips, I can save the project as a bundle (CWB). When saving as a bundle I get prompted with a message that indicates this will wipe out all cached transient edits and I click OK.
 
When reloading the project file (not the bundle), I get a message that it is re-generating transient markers.
 
Finally, I go back into the problem snare track and I have normal looking transient markers again. The problem is that I lost all my prior edits and have to start over with moving the markers.
 
I guess my transient marker cache got hosed up somehow and although it's a PITA, I have a way forward...

I have seen this with AS clips in older projects. If it happens again (or if you still have a copy of the project with the edits in place), you have a few options that are less drastic than dumping all edits on all tracks:
 
1. Bounce to Clips only the affected clip. This will render any stretching permanent and regenerate markers.
 
2. Right click the clip, choose Associated Audio Files, and Recompute Pictures. This will dump the edits only on that clip, and regenerate markers.
 
3. Disable Audiosnap on the Clips tab of the Track Inspector for the affected clip, and Bounce to Clips before re-enabling AS. This has the same affect as option 2, discarding any edits on that clip, but is more likely to work than Re-compute Pictures as it actually re-writes the audio file before re-detecting transient markers.

Thanks for the reply. I will give your suggestions a try the next time I run into the issue. I'm only trying to generate MIDI notes for drum enhancement/replacement on two tracks (no audio stretching), so I was only redo'ing one track since it was the snare track in both instances (kick was done/good).