Melodyne edits as Region FX are not cloned with the track.  Cloning a track needs to clone every single thing in the track.  Cloning a track with Melodyne VST keeps the edits.  I hope this isn't a limitation of ARA.

As a vst, the melodyne processing is done after the audio is recorded ie not in real time.
In region fx using ara it is live. Would be like trying to clone a track that you were still recording.

The whole thing about ara is giving a plugin access to audio data for real time manipulation. Under those circumstances it doesn't seem logical to expect to be able to clone it. You can't copy what is not yet done. If you are finished the melodyne processing bounce it then clone. Why??

Actually Melodyne as a region effect is identical to it as a track effect - it has to read in the data and store information about the desired edits.  It's not at all the case that region effects are "live" - only that they are given access to audio data as data rather than as streamed audio.
 
Clip effects are cloned - region effects should be treated like clip effects in this regard.
 
An obvious reason for wanting to clone a track with melodyne on it is so that you can archive one version with some editing, then make further edits while having a "safe" copy.  Another reason is that you might like to make "harmonies" from the track, and in that case it would be useful to begin with the already-edited master take.  Another reason is that Cloning tracks is one of the great features that makes Sonar a program worth using, and that another of its great features - ARA - is incompatible with it is a big blight on the program.
 
 

Actually cloning a track with Melodyne edits completely screws up the edits on the original track, as well as failing to clone.
 
This turns out to be a major oversight of the ARA implementation and at a minimum Sonar should prevent Cloning of tracks with unrendered region fx, although that minimum is not nearly good enough.

I've had some problems with the ARA implementation as well and I suspect it needs some more work doing on it. One thing I've noticed - and I don't know if anyone else has seen this - is that if you create a Melodyne clip and then insert measures behind it, the clip is shifted along the timeline along with everything else but the actual position of the audio doesn't move with it. So I've had cases where I've inserted measures in a project and the Melodyne clips started playing at the new position of the clip, but at the point of the audio that would have been playing before the measures were inserted (if that makes sense). I also had a case where I shifted the entire project to the left in order to fill in a blank space at the beginning, and the audio in my Melodyne clips just completely disappeared. The waveforms were still visible in them but when I played them I got silence, and when I bounced them to clip I got empty clips. I had to undo everything and bounce the clips first before moving them. 
 
I'd love to know how well the ARA integration works in Studio One and if users over there have experienced any similar problems. 

Obviously I can't explain myself as well as I'd hoped. I'll leave it at that.

A thread about melodyne with comments by Noel about track cloning.

Interesting.  Well, at least Cakewalk is aware that it is a problem that needs fixing.  I believe that thread was from the X3b era, though...
 
There's so many different purposes and usage scenarios to all of this.  Any given action will seem unnecessary to some people, and essential to the creative process to others.  I think the aim of the programmers should be to make something that is versatile enough to satisfy many different processes, without getting too far into the weeds of course. 
 
However, this sort of core incompatibility between two bedrock functions of the software needs to be addressed somehow.

Clearly it was me that didn't understand the ARA possibilities. Having thought about it some more, I wonder If it works in Presonus Studio One V2. I'll have to install it into my studio DAW and see. Because if it doesn't work in Sonar because of missing code then it should work in studio one.

It begs the question then; is the missing code that Noel mentions going to make it into x3d?

I suspect we must be getting closer to a release for that as gradually the baker's presence here is diminishing.

Melodyne implemented as ARA also prevents Groups in U-He Satin tape plugin from loading when re-opening a project.