So, this happens:
 

 
Sorry the gif is small but it's the best I could produce. I split the midi track, move the segment a bit and the rest of it disappears!
 
Note: this happened on one occasion when I decided to use Sonar for a job with a client who was with me (I usually only use it a personal song writingtool). Of course it's a very embarrassing thing when a chunk of music disappears while your client is breathing down your neck.
No I don't know why, yes luckily I can UNDO, yes it keeps on happening, no I can't do it in SONAR then. 
Export tracks, change settings, the flow of the session is interrupted. I know things happen, but I'd do without all the extra fiddling AND the comments of the guy who's paying for studio time
 
And I'm frustrated because I would REALLY love to use Sonar for my day - to - day work and I have to stick to another DAW which I thoroughly dislike because of those glitches
 
Thoughts?

I'm not sure exactly what happened there, but would suggest the following:
 
- Disable 'Non-Destructive MIDI Editing' in preferences.
- Show lanes and manually move clips to separate lanes if you want to the result of an overlap to be sound-on-sound playback.
 
 

Also watch out for the "Replace Old with New" in the Drag and Drop Options.

And never use "Slide Over Old to Make Room" in Drag and Drop Options (although this looks more like the "Replace Old with New" behavior).

Thanks guys - I'll try fiddling around with the preferences.
 

Jordan, just to be clear , you are splitting the clip then dragging the first part of the clip then the last part of the clip disappears?
     this does happen to me as well.

Good point on the Drag and Drop mode.  I almost forget these other modes exist. I pretty much always have this set to 'Blend', and I delete/move clips in the 'landing zone' manually to get a 'replace' or 'slide over' result. Letting SONAR (or any DAW for that matter) re-arrange your music with such rudimentary logic is unlikely to produce a desirable result in most cases. Maybe somewhat more likely if you're working with loops that are all nice, even, 2/4/8-bar chunks with quantized start times.

This has happened to me plenty of times, And changing to Blend usually is the only one that will work.  
It's always eluded me why rearranging a whole song ( midi ) is such a chore in Sonar.   
 
 

David
Jordan, just to be clear , you are splitting the clip then dragging the first part of the clip then the last part of the clip disappears?
     this does happen to me as well.

Yes that is exactly what happens

ever try bouncing step sequencer clips to normal clips and find it deletes like half of your step sequencer clips?   yep.  I can confirm I have had the same issue as the OP too.

I notice that if I try it a few times, sometimes it just works (with no changes being done between attempts).

OP, have you seen that?