Melodyne has stopped allowing me to edit multiple tracks from a single instance. I can still use ARA mode with multiple tracks, however I have a project where I want to edit large portions of several tracks altogether, and ARA mode has proven to be less stable for this use and also really bogs down with lots of blob information.
 
I have used the plug-in version on multiple tracks before, and even referenced a previous project where I had used it. However on my last 2 projects, I loaded multiple instances, and each one only showed the selected track in the pane. Any ideas?

It sounds like you have done this before so I don't know if this is going to be much help.  In the view menu, I think, you open the view to see the other tracks. When you do this do you see the other instances?  if you don't then I don't know what is going on. If you do then you have to click on the icons by the tracks to make them show up.
 
Let me know if you find a solution.

I didn't see any View menu. However, I'm using the plug-in, not the stand-alone version so it may be different. I got them to consolidate by restarting SONAR. However doing so caused them to lose the track names (i.e. before they were Guitar & Vox, and now are Melodyne #1 & Melodyne #2). Something is definitely a little off with it.

So you're not defining a region fx clip? That's the only way to get benefit from ARA.