It IS a single clip. It is one clip in one take lane with nothing else anywhere near it. There is nothing there to flatten. It is a bug.

Look, to end the debate over it being some invisible clip that somehow is getting selected and is linked to an arbitrary number of other clips, here is the same operation with take lanes expanded, where I operate on exactly and only one clip, and Sonar toggles a bunch of others for the hell of it.
 

It's just ridiculously broken.

(deleted double post)

But it is likely auto grouped due to the comping feature (and you don't need your record settings to be set to auto group... the comp/smart tool does auto grouping stuff as well as soon as you make splits and whatnot). If you opened the lanes to observe the actions taken during selection and editing you could better assess what is going on. I can only make assumptions as to what is happening from the gif because Lanes are not visible so I cannot even begin to say exactly what may be happening.
 
Not trying to give you a hard time. I'm just saying editing in the parent track is likely the problem here. It just does not work in any reliable/traditional way because it's no longer designed to do so.
 
Crack open those lanes, give 'er a good inspection (and maybe take some more animated gifs) and perhaps it will reveal a bug. There is indeed some quirky stuff that happens sometimes but this, to me, all seems related to editing in the parent track. Been through it myself which is why I'm saying all this.
 
Cheers.

See above.

Kylotan
(deleted double post)

Okay. Thank you. Zoom out and check the Clip Group numbers. I'm willing to bet those clips are in an automatically created selection group. If they are in the same group which is causing them to respond to the unlock action.
 
And there's no debate or argument. I'm just trying to help. Like I said... I've been through this.
 
Cheers.
 
Edit: And since they are in the same lane perhaps, even if there isn't some grouping stuff going on, it has something to do with those segments all referencing the same audio file. Like the original clip was edited to have those gaps so that is just the project rendering of an entire clip. Now it's forcing all the clips referencing the file to respond to these changes.
 
That... to me... does sound buggy BUT I am not sure if that's the case or what the heck is going on. Really you shouldn't have those gaps in one lane in the first place. There should only be ONE clip per lane with no gaps. Instead of gaps there would be sections that are audible (promoted to the parent track) and muted (invisible in the parent track which makes them unavailable for editing from the parent track).
 
So something ain't right but I think it's a matter of you deleted those sections.
 

There are no clip groups. I don't record in comping mode, I don't record more than 1 clip at a time, and 99% of my MIDI clips are not recorded at all, but are dragged in from loop libraries.
 
But, again, just for the avoidance of doubt, here's me ensuring the clip is not in any selection group, repeating the lock-toggle from the expanded take lanes, and seeing a bunch of other clips change state in sympathy.

 
Regarding your other suggestions:
"it has something to do with those segments all referencing the same audio file" - no, they're completely independent. They're not one big take sliced up into bits, they're different files created by EZPlayer.
 
"Really you shouldn't have those gaps in one lane in the first place. There should only be ONE clip per lane with no gaps. Instead of gaps there would be sections that are audible (promoted to the parent track) and muted (invisible in the parent track which makes them unavailable for editing from the parent track)." - This isn't a comped track, so it's never going to resemble what you describe. This is a song composed by dragging a bunch of clips together, some with crossfades, some adjacent. Sonar has made these extra lanes automatically on my behalf, presumably in some misguided attempt to help when there are overlaps (which are often only temporary, pending me slip-editing a clip).

Warning: This is getting out of my comfort zone because I mostly work with audio. Just some stuff to check or maybe get the other users to come up with solutions.
 
===========================
 
hmm... it's MIDI so something else may be going down. I don't work with a ton of MIDI and when I do I usually bounce to one clip.
 
These aren't Step Sequncer clips? Right? It's MIDI?
 
Is this affecting clips in other lanes as well?
 
If you move one of those clips into a new/empty lane does it still respond to the unlock/lock action (or other actions)?
 
And this one is a total guess but maybe this is due to the clips getting crammed into the same PRV clip and they need to be unlinked somehow. I've had a bear of a time in the past trying to get unwanted data out of my PRVs before and it has manifested itself in the TV.
 
 

No step sequencer clips.
 
It doesn't appear to affect clips in other lanes. Of course, I have to unlock a clip in order to move it to a different lane which means it's already toggled a bunch of others by that point. And it doesn't toggle every other clip in that lane (so it's not like it just thinks 'every clip in this lane is basically the same clip') - it just seems to select a few of them, apparently always ones that are linked (but not to the clip I am toggling - that is usually unlinked).
 
I'm quite used to MIDI data ending up in the wrong clips. Sonar makes things very awkward when I edit in the Piano Roll because it'll often associate my new or moved notes with the wrong clip (eg. extending a nearby clip instead of creating a new one, or extending a clip backwards instead of adding to the end of the previous clip). That's exactly why I have to lock clips, to avoid damaging them in this way while I edit. However, I am confident that the clips in question are separate ones. They have separate names in the track view and the inspector and were created independently. The only thing they have in common is that they both would have been dragged in from EZPlayer.

I've probably exhausted my usefulness in this thread now that we've dug down into the lanes into the individual MIDI clips. Gonna have to let the MIDI guys/gals troubleshoot (or bug confirm) from here.
 
I would still suggest trying to move one of the misbehaving clips into another lane (or even track) by unlocking them, moving them then seeing if they behave to selection edits as they would in the same lane (and/or track).
 
I am totally ready to admit that this particular behavior on these MIDI clips is a bug/unwanted manifestation of the comping stuff.
 
There's a whole swath of screwy, unwanted stuff that happens with clips/lanes/parent tracks when I don't completely adhere to the "comping" pardigm from the very start (tracking to final editing and flattening). I essentially just accepted it as the new way to do stuff, learned it and adhere to it and mostly get what I want done. I do however work in some odd ways that results in some unwanted crud happening that I generally have to go through and clean up before going apeballs on editing (like recording slews of takes in multiple sessions and/or one section at a time instead of all all at once and spanning the entire song).
 
It really is quite complex once you break out of the established guidelines so I feel your pain. I just can't quickly explain in text all the things I do to avoid it (and it's all different between audio and MIDI and depending on how the tracks are being recorded).
 
All in all though, once I got it, it's a good system. Just a somewhat f*cky one. I like it way better than layers and the original X2 lanes.
 
Once MIDI gets involved things get even crazier due to the strange disparities and forced linkage of clips in the various views. I'm still sorting out the nuances of all that (because I record/edit/comp live MIDI as if it is audio and it gets soooper stoopid). Again though in those scenarios (and even more so than with audio) I completely enforce Bouncing or Flattening to a single clips and make absolutley sure the ONLY data contained in/linked to that clip is what I want audible and editable. This definitely requires totally getting rid of the comping track by archiving it and putting the fully comped/bounced clip in it's own track.
 
Just my brute force ways of making it happen. Totally hard to explain and often times the solutions change based on the material (and how I f*cked it up... lulz).
 
Cheers.