I've had this problem before and it drives me crazy. I've just recorded an audio track (bass guitar) in Sonar Platinum and want to move one of the notes in the middle of the clip slightly later than I played it. I cut the note in question on both sides and dragged it along the timeline a little, but as soon as I moved it, the rest of the clip (which I don't want to move) just disappears. I tried changing the Recording preferences to Sound on sound and Comping but these had no effect. I tried moving the beginning of the rest of the clip away from where I was moving the individual note but that didn't stop the rest of the clip from being deleted either. Any ideas? Is this a bug?

You might be moving a clip that is under another clip so it is difficult to see (to know if another one is there).
What I typically do is use the "Bounce to clips" function.
This way I know what im dealing with is a whole clip and not fragments underneath.
 
Once you know you are dealing with a whole clip it is much easier to know what you are editing.

Also, make sure when you select the clip you want to move that the other clips don't get selected as well.

You don't have ripple editing enabled, do you?

I'd like to know if ripple E is to blame. I've had unwanted behavior similar to this with Sonar since X1. There's so many optional variables anymore it's hard to know if this odd behavior is due to a setting or a bug.