Jlien X
Hi Beep. Sorry, I didn't have time to read that thread. I haven't explored comping mode yet, but I've just tried the steps above using comping mode and I still see no problem (maybe I will if I try more?).
Btw, you can drop u because I'm actually not Julien. 
Oh... lol. Sorry about that.
You know I was going to try explaining what was going on and getting you to try the "Hide Muted" option but now that I'm thinking about it more none of it makes any real sense the way it was happening to me. Trying to gather my thoughts on how to explain it but I think something is definitely going weird with my project or something.
Edit: Just for clarification in the steps below I am manually entering MIDI notes into the PRV using Alt + Click or double click with the Smart Tool selected.
So here's the deal. I had created a flattened comp and cloned it to give it its own track and deleted everything else.
I created a copy of the flatten comp so I could use it to compare the original with whatever edits I made. I Muted the lane AND the clip of the original.
I selected Hide Muted Notes from the PRV context menu so the original clip (now muted) would not appear in the PRV.
I selected the clip I wanted to edit > Right Click > Views > PRV (or alternatively double click the clip).
Sure enough only the notes in that clip were visible and the notes responded to editing.
So that's the first part of the recipe. Here's where it gets weird.
When I'd enter NEW notes in Comping mode they would be visible in the PRV but not play. I could see the new notes appearing in the PARENT track but not in the selected clip. No new Take Lane was appearing.
I switched to SoS, inputted some notes and they WERE audible but still not appearing in the clip. Only in the parent track. I still hadn't fully grasped what was going on so thought I had solved the problem. I close the project without saving and reopened it to get back to my starting point. Now SoS wasn't working.
Now I mentioned that I saw the new notes in the Parent track but actually I had NOT. I didn't figure that out until this point of my struggles BUT this is reliably produceable behavior so I know it was happening. Just tossed those in there for clarity. After doing some tests to find out WHERE the new notes were going is when I saw them going into the parent track but not the clip(s).
So I tried closing and reopening the Lanes section and TA DA!!! there was a new lane with a new clip that contained the new notes. However the Take Lane Mute button was engaged making them inaudible.
Let's ignore SoS mode for a second. Now initially I figured that in Comping mode this made sense because Comping mutes all other takes and solos new material but that DOESN'T make sense because then would the new notes in the new lane in the new clip be audible and the clip I was working on get muted? This is muting the NEW material so it does not follow Comp mode's expected behavior.
Now for SoS... this should leave both the original take and the new notes audible but I only managed to get that to work once and it was before I figured out the lane thing. I did check again quickly after realizing that a new lane was being created and that new lane had indeed been muted.
I have not yet tried Overwrite to see how it behaves but I am assuming it would either allow me to input new notes without a new lane or effecting the other notes OR it would delete any notes at that same point on the timeline. If it is the latter it may indeed be the better option for this type of touch up editing.
So maybe it's just this project or my system or I've got a weird setting or I'm forcing Sonar to work in weird ways that the Bakers didn't anticipate or maybe I found a bug.
I know you like to explore these types of things so there is the recipe and the results.