I have a Battery drum clip that I've been working on in the step sequencer (although I think I may have messed around with it in the PRV as well at some point). It was puzzling me why certain snare hits sounded louder than others when their velocities are exactly the same. 

So I deleted an offending snare hit in the step sequencer, and to my amazement the hit was still sounding. So I took a look at the clip in the PRV, and sure enough there's a note there despite me having deleted it. It looks like there was one snare hit on top of another, although that obviously wasn't showing in the step sequencer. 

But I cannot delete the snare hits that were "underneath"! In fact I cannot do anything to them. The smart tool does not change when I hover over them. I cannot move them. I cannot adjust their velocities. They are just baked into the PRV and untouchable. The clip is basically ruined unless I can get rid of these damn poltergeist notes. Any ideas? 

Gahh what an idiot. I seems that somewhere during my haphazard drum editing, I've laid one clip partly over another, without bothering to shorten the clip underneath. The notes I could not touch in the PRV were actually in the clip underneath. Chalk another one up to my unstoppable genius. 

Tip: If you suspect you might have duplicated notes, take a look at the track in STAFF view.

Any duplication will be immediately obvious as both will appear, one either side of the stalk

Tip 2: If you delete any of these duplications, you'll he horrified to notice that this action deletes BOTH notes - don't panic! Just hit ctrl + z and you'll see just ONE note restored, exactly like it should be.

I don't know if this is a bug or by design, but it's worked this way since at least version 6PE

That's actually a good tip.

Since the begining of time (did time start with Cakewalk 3.0?... At least it did for me) I have had midi notes that have behaved as you suggested, you can not delete them.  Sometimes it is just duplicates for some reason or another as happened here...some use to have duration times of "zero" and sometimes when you edit lyrics dupicate notes show up.  There are a variety of situations that would cause these notes.  In X2 occasionaly I have "fantom" notes I can not select to delete.  It always seems that perhaps one way of deleting will not work,  but an alternate way will. So selecting them with the smart tool and hitting delete on the keboard might not work,  but highlighting an area on the timeline and "cut" might..or vise versa.  The worst case I think is you have to exit out of Sonar and then get back in. 

I'm not sure i'm contributing to the conversation here, but I thought i'd toss in my observations on this subject.