Is there a way to have two instances of Sonar open at the same time?

Assuming that they have not changed this, the setting for allowing more than one project open at a time can be found under:
Preferences > File > Advanced
 

You can copy/paste track content (not tracks) when you have two projects open in a single instance. You can arrange them in columns for easier dragging and dropping. There is no need to have two instances of Sonar open for this and in fact you can't.

Ok, what issues are you having with save as?
 
It should be relatively straight forward to do what you want.
 
Are you attempting to open a bundle file or a cwp?
 
If it's the latter, what happens if you start Platinum and open your project from there?
 
This is by far the easiest method so if it's not working for you we need to try and find out why.

X3e is really quite stable. I'd suggest getting it working properly, opening your projects in X3e, and "save as" using per-project folders. Then open those in Platinum. I've had no problem opening files created in X3e but then again, didn't have problems with X3e originally.

Thanks Craig, Brundlefly, Sanderxpander and Cactus Music, for your thoughts and suggestions while I've been sleeping. I am trying to work through all of them and see what happens.
 
 
So far today I have opened the project in X3, trimmed and bounced every track so that there is only 10 audio tracks (and 2 midi) to make sure it is as clean as possible, and 'saved as' to a new file on another disk. However, in my newly created audio folder, 31 audio files still appear when there should only be 10! I can tell from listening to them that many of them are from 2-3 years ago when first writing the songs, yet are no longer meant to be part of the project.
 
When I remove one or more of those files from the audio folder and open the project, I get missing audio file messages. I'm told that audio will be replaced with silence. However, none of my tracks is missing though - as the file it is seeking is one of those really old early versions. Even though I skip the file search and save as such, the project is forever wanting to still find those missing files. (Hence, as mentioned in my experiment above, I can reduce the project down to 5 sec of audio on one track only - save it, yet still produce a 1.4 GB Bundle file!!! ... if I try that option)
 
I really just want a clean project as I believe those 'uneeded' 'missing' files are a big part of the reason I've had issues with these projects in X3 in the first place. I just want a clean version in Platinum, which is why I was trying the cut/paste alt/tab method to see if that would avoid the baggage.
 
When I've tried having the two projects open in one instance of Sonar as suggested (arranged in columns, and copy/paste between them) - I get crashes!
 
I will continue trying some of the other suggestions today ....

Scook - you are a legend! and I feel pretty stupid! ... I found hidden tracks!
Hopefully, when I delete these, the project may behave better. I'll try this out today. I'm off now to buy my son a keyboard and audio interface etc.
 

Keyboard, audio interface and headphones purchased - kid rockin' ... Now my saga continues ...
 
After managing to get X3 working without crashing for a few moments, I removed all the hidden tracks except for one, and then saved the project and its audio to another drive. I opened it in Platinum and most things seem OK ... except this ... 
 
My one remaining hidden track keeps getting hidden again and my current view is not maintained. I click H, make sure the particular track is not hidden, ticking the checkbox to keep track and console visibility in sync, and save the project in console view. When I reopen the project, the formerly hidden track is again hidden (track manager shows it unchecked) and my current view is track view rather than console view where I saved it. I can repeat this over and over. This would at least explain why my hidden tracks got forgotten at some point along the way when cleaning up this project.

Yes!!! Thanks Brundlefly! Another box ticked off!
Although the strange thing is that I have never used screensets, ever, so just didn't consider such a possibility. I only use  the D, I and B keys to change things according to my needs. 

There really is nothing to worry about.
 
As you can see from the above exchange, and without being rude, all of the problems were down to pilot error.

I have gone through all versions since Home Studio, S6-7-8.5 skipped X1 and X2 a then X3 and now Professional. 
ALL my CWP files open and they all have played. If I open an old CWP from S7 which was 32 bit and a different interface I get the missing plug in warning. They still open and the missing plug ins will show in brackets in the effect bins. Just delete and replace with a new one. 
You get a warning on opening about what has changed, that's all. Midi is Midi , audio is audio. 

Yes Kev, but certain features added in later versions, for example ProChannel, Melodyne, will not work