Save the relevant portion of the project as a new project to a new folder, zip it and send to us. We may be able to see whats causing the issue and fix for the future.
In Platinum there is also a new feature to clear all AS markers in the project if you wish to recover it. You have to right click the AS button in the AS toolbar to get to that menu item.

Hopefully I'm not necroposting since the post has been resurrected...
Having most of the same issues described at the beginning of this thread, they just started occurring.
 
Using transient markers, when zooming in all the markers disappear.  (1) When the cursor passes left/right relative to the track in question (even if not over the track) then many of the markers disappear / reappear.  (2) Occasionally if I pass right and pause, they'll reappear if I just wait a bit.  (3) I can only add one or two transient markers but not what I need to add, and not where I need to add them.
 
This is only happening in one guitar track, not in my other tracks.  However, interestingly I have not had this project open since late May, at that time I was not having this problem with transient markers on this track.  I just upgraded to Foxboro before re-opening this track, and went to finish the editing and now this is occurring.  Doubt it's related to that since it's only occurring on one track.

I just dug out the original clip of the offending track from a backup and pasted it into the current project - everything seems to be working fine.  Appears to be solely related to a corrupted clip somehow.

@MorganT... Did you save the project with the audiosnap/transient changes open? As in did you not bounce your transient changes before saving and closing the project?
 
This is indeed an old thread but I have learned since I originally posted this that if you do things like AudioSnap, Melodyne/VVocal or any other "region/wave manipulating" type work without bouncing BEFORE closing then problems arise when you reopen the program.
 
This is not documented and it should be but really when bending the raw waves with stuff like audiosnap or melodyne it is best to do it in increments (split the clips, work on a section, bounce/render the changes) and only save/close the project once you are totally done.
 
I think what happens is when you reopen a project with open wave manipulations Sonar and the system gets freaked out and strange things start happening. Like it is just too many calculations to deal with all at once (whereas if you are doing it just one transient at a time it has a chance to think/do the calculations).
 
I would personally LOVE to see Sonar get stable enough to allow open, unbounced, wave manipulation to be saved and reopened but I also think this requires an absolutely top shelf system... particularly the drives in play.
 
I think 99% of the lags, quirks, freezes I experience are due to hard drive stuff or perhaps poor HDD management by Win7 (I never upgraded to 8 but may try Win10 after I see it is stable and not a joke).
 
Meh... I'm a little scattered to day but really the fact your original wave worked fine kind of confirms my su-s-p-i-c-ions Sonar can't handle unbounced AS stuff. I'm sure the "old project from an old version" factor doesn't help. 
They supposedly fixed up the AS engine a bit with the release of SPlat but I don't think this was part of the overhaul.
 
So... my long meandering crazy guy post essentially is meant to say... do your transient edits using AS and BOUNCE them before closing the project. Do it in chunks if you have to.
 
Cheers.

No, I didn't bounce at all - didn't see that in any of the documentation on Audiosnap/ Audio Transients, so I just assumed it was rendering the wave maniupulations as a new clip whenever I stretch/move Transients.  I have always bounced each clip when using Melodyne or V-Vocal, but that's pretty obviously still sitting there as a manipulated, unbounced wave until you do so.  I do always use shorter clips for the manipulations too.
 
What you suggest may be the problem - but the other tracks I had also manipulated all seem to work fine, it was just this one track.  I have had more than my share of Sonar crashes of late, I wondered if perhaps one of those somehow corrupted this track...

I DID notice that the markers seem to still be present, just not displaying.  If the cursor by chance hovers over an invisible marker, it will change to the "move" or "slide" cursor shape.  Made me think it's a display issue as per the original suggestions - but it's still related to certain tracks and not to all of them.

I had some odd behavior with this just this week.
 
I spent an evening working on AS with 2 acoustic guitar parts. Saved the project and the next day I opened it and the transients would disappear at some zoom settings... but only on one of the tracks. The other track displayed the markers just fine.
 
Even though the markers were missing they were working so this is a visual thing.
 
After fussing around with it I managed to loose all the edits on that track. :(
 
I was able to redo the work in short order after I disabled as for that track bounced the clip and then enabled AS again.
 
So far (knocks wood) it has not repeated this problem.

I should've thought of that - I've on occasion had trouble with Melodyne functioning properly - I found if I bounced the clip and then re-opened it in Melodyne Editor everything was OK.  That would have been a lot easier than pulling in all the clips from the original tracking!

I think really on an ideal system under ideal circumstances we wouldn't (shouldn't) have to worry about such things but let's face it... we are all working on various PC configs (and those who aren't... like the Bootcampers are even worse of than better). My rig is good but I built it myself and I am no DAW builder. Most other are working with off the shelf stuff that's been tweaked or have done like I did and built their rigs themselves. Then there's hardware and blah dee freaking blah... that adds all sorts of complexities.
 
If I had my druthers I'd be running a professionally built DAW tweaked to specifically handle Sonar and all my various outboard crap and a/d converters.
 
When you think about how insanely complex things like audiosnap/melodyne calculations must be in the grand scheme of things (we are what... like only fifty-60 years removed from lightbulb and punchcard computing... lulz) then it makes sense that the program may vomit all over itself on a consumer or even "prosumer" PC.
 
To me I think my issues are HDD related and an inability of the DAW to recall such inticate silliness fast enough. The CPU may be willing, the RAM may have enough space but something somewhere is bumpling about and borking things up... so I just try to be careful and aware of the limitations of my personal home technology.
 
I would like to point out some of the videos on this very site produced by Cakewalk themselves on their own ultra tweaked, high performance machines. If you look at the old CakeTV Drum Production webinar with Seth and Ryan (or other vids here and even on Groove3) you can see some of these strange graphical glitches occuring with Audiosnap (and other areas of the program).
 
I recognized those little glitches immediately as I saw them but seeing how various doods just hammer through them gave me a little hope and I've learned to somewhat ignore them but also be aware of them as indicators that PERHAPS something was about to go all crashy smashy on me. Which is why I Save As repeatedly so when it DOES happen I've only lost maybe 5-20 minutes worth of work instead of 4+hours of work (which is what happened when I originally posted this thread).
 
I bounce and archive and freeze and watch my synth/vst count. I try to make sure I don't allow my project to have a million tracks with a million active takes. I keep the performance module open whenever possible to keep an eye on resource consumption. I micro manage all the other processes that might be going on on the system (like antivirus stuff, auto updates, internet/network weirdness).
 
Essentially I treat my rig like a living entity that b*tches and moans and cries and wheezes when I'm abusing it. If I listen and try to not kick it in the teeth any more than I need to I can get things done. If I don't... well there is a whole wack of hair pulling, screaming and running here to the forum to kvetch and try to sort out WTF I did wrong (which is time consuming and not pleasant for anyone involved).
 
My point is... don't temp fate. Before doing things like AS manipulation do a Save As, make a plan, do a bit of experimenting to see how that plan is working out and how your system is handling it THEN do another save as and start the work proper, do it quickly and in chunks bouncing and Save As'ing as you go.
 
It's annoying and semi time consuming to do things this way but since I've gotten ULTRA paranoid and cautious about stuff like this the amount of time and stress I've actually SAVED from avoiding epic catastrophes MORE than makes up for adding those steps into my workflow.
 
Sonar works better and better every year since I've owned it (like WAY better) but in computer terms we are essentially putting a man on the moon with some of these "simple" tasks we take for granted every few minutes or so.
 
Just taking a break from my tracking so I sorry for the long, boring, pseudo-philositechno post but really... unless you can buy a dedicated DAW built by a DAW builder caution and awareness of what your system is trying to tell you is advisable... and even if you do get the ultra high quality Studio Cat custom builds you still should be careful.
 
Cheers.