Jyri T.
Fair enough, it works for some (most?) occasions, but if you have a longer clip, it may turn into a bloody mess.
 
You may find yourself with a sea of phantom transients, which don't go away yet won't engage. You may find yourself with a sea of tiny "user" transients that you never put there. You may find yourself with clips that won't let you make a transient. You may find yourself with hidden double ("twin") transients that will not let you stretch the audio. Etc.
 
The longer the clip and the longer you work with it the bigger chance for these mishaps.
 
I can't always use the "double click the transient" feature since it enables also "hidden twins" for the transients I'm aiming for. And I can't use the "ctrl-double click" at all since it doesn't do anything for me.
 
So, I did read the manual yet I still have problems that should NOT be there.

 
- Merge and Lock markers is what you want to use to maintain phase. But it takes a lot of work to get to the point where you can do that and have all the markers you need in all the correct places with no dupes. I don't think it's ever going to be "easy" to re-time 8 tracks of multi-tracked drums without introducing phase issues. And Audiosnap certainly has some issues that "shouldn't be there". Some thoughts/suggestions:

- Not sure what you mean by "phantom transients...?.
 
- The superfluous User markers on beats can be selected and deleted (bind a key combo to Delete Marker so you can just hold it down  after selecting all User markers and let it iterate until they're all gone), and it was recently brought to my attention that they go away on their own if the clip map tempo roughly matches the actual audio tempo. If it's mis-detected, setting the correct tempo in the clip map drop down should clear the User markers.
 
- I use Alt+click to insert User markers.
 
- Normally I would not expect to have an issue with hidden duplicate markers if you're zoomed in enough to accurately place your own, but it pays to do a quick visual scan of every clip at a zoom level sufficient to see all the markers before you start working so that you have an idea where the transient detection issues are.
 
- Splitting clips as Ron suggested might be a good strategy to try, especially if there are only particular sections that need work.