Strange comping behavior

Right-click on the Comp Clip in the parent track with lanes showing, and choose Flatten Comp. This will create a new lane with all the active clips in comped lanes rendered into one new clip. The comped lanes can then be deleted. Note that the Flattened Comp clip will be locked by default; if you want to do further editing, you'll need to right-click and unlock it. Then close lanes, and you'll be working with a 'normal' track. I suggest you do this on a clone of the track (or a copy of the project), to allow recovering the original clip/take structure later on if needed.

 So I think I have this all figgered out now. The crux of my biscuit I do believe is deleting the muted clips. If you retain the unused portions of your comp track, these unused parts will exist in a layer below the used portions and if/when you do any editing the unused portions become a major nuisance. If you slip edit a phrase out of the song, for example, then you will see the unused take of that edited-out take beneath the clip as you slip edit. This can be confusing. While the exposed unused clip seems "grayed out" and I'm not sure it is audible, it IS possible to delete the unused track beneath the used comp track, and I REALLY don't want to be seeing waveforms that are silent (even if grayed out). This is really confusing! The big biscuit is Melodyne. When you Melo a phrase on a comped track which still has the old takes remaining beneath the used takes - best case scenario is that Melo will properly edit your clip but will leave a blank clip ON TOP of it (I won't swear the blank clips were actually blank as another user indicated that redrawing waveforms on these blank portions showed them to contain audio - so quite possibly the "blank" clips I deleted were actually the Melo'd clips and the clips beneath were actually unused takes from comping that I unwittingly brought back into the fold) or perhaps Melo is a bit confused(?) by what it may (rightfully) perceive as multiple clips in one track. I also encountered some corrupted phrases after Melo'ing and the only way these corrupt phrases could have come about was through Melo - as they were split individually and consistently with my methodology of Melo'ing line by line to avoid a) overworking my computer b) ensuring all changed notes SHOULD be changed. (It takes a major leap of faith to Melo a whole track at once, right? A note or two correcting the wrong way etc...) I deleted the corrupt phrases - just three fortunately, but now whenever I open this project I get a "corrupt audio file detected and replaced with silence" message. 
 My second flash of <s>genius</s>,er, stupidity correction, was the realization that all tracks are comp tracks. Any track can be used to comp, so my quest to convert a comped track to a normal track was a bit misguided. I will be deleting unused clips as quickly as I confirm they are unneeded from now on. 
 And yes the clip being locked after flattening seems counter-intuitive but perhaps it is good to be reminded that it was a comped track and MAY contain extraneous information in the tracks below - proceed with caution! 

stevesweat
And if you bounce to clips a comped track with unused lanes intact the bounced to clip will still contain those unused takes (I'm 95% sure I encountered that behavior)
 

 
That sounds like the result of using Bounce to Track(s) rather than Bounce to Clip(s), and specifying the source track as the target track.
 
Bouncing always writes a single new audio file and creates a single new clip referencing that file. In the case of Bounce to Clip(s), the original clips will be deleted, and the the file(s) referenced by those clips will be 'orphaned', though they continue to exist in the project audio folder.
 
But if you Bounce to Track(s) with the source track as the target, the original clips and take lanes will continue to exist, and SONAR will drop the new clip on top of existing clips in the uppermost take lane if you don't pre-create a new empty lane to hold the bounce.
 
Bounce to Track(s), specifying a new target track, is another way to flatten a comp, but only if the original track doesn't already have altered Gain/Volume/Pan, Sends, FX etc. on it.