Audiosnap transients flaking

I thought most of the graphical glitches with AS transient markers had been fixed by X3e. When it does happen, changing zoom level will usually make them visible. I've never seen Audiosnap move a transient without being commanded to in some wa, so on that basis I would say, no, it won't ruin a track by itself.
 
If graphical issues cause you to mistake which transient goes with which beat or if the changes you make are too radical or based on misplaced markers, the results can be bad. But so long as you don't render any changes permanent, you can always reset markers or disable Audiosnap altogether and try something else. That said, it's always a good idea to start with a copy of the project (or of an individual track that you want to snap) so that you can easily fall back to the un-snapped version if you don't like where it's going.