I think the answer is in the OP sorting out the saving of projects. You living dangerously if your files are that unstable.
I think what's happening is you just haven't got your saving figured out.
 
 
I would be using my DATA drive to store projects and Audio. Never use Cakewalks default unless you want everything jumbled up in a big mess. 
If there is no second data drive then use an external USB  drive.   
Open a  project in X3e.
Go to file
SAVE AS
 
Now browse to the data storage location using the windows dialog boxes ( save in) .
Check the "copy all audio with project"
Make sure the file type is set to Normal for best results.
 
No need to rename the project but if making back ups this is a good idea using a date.
Now hit save. Done deal. 
If transfering to a new computer simply drag and drop the folder(s) to your new Sonar folder locations. 
I use a data drive and have main folders for each album/client. 
Now open your new version of Sonar/ file/ open/  and browse to the data storage location to open. 
 
 
For the record, you can have dozens of projects open and minimize them to the bottom. 
I have copy pasted this way plenty of times. It's just windows. Sonar is a windows based program and copy paste between windows is standard stuff.  Now 2 different versions? That has never come up for me because my projects have always opened in the newer version abet with a few warnings about missing stuff. 

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 ....

Could the project have hidden tracks? Type "H" to open the track manager.

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.
 

Scook is...
Get that kid of yours rockin!

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.

Locked screenset?

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. 

Wow.  This thread has made me paranoid.  When I upgrade to Platinum tomorrow and find out I can't finish the Projects I'm working on that WILL REALLY SUCK.  As in on a scale of 1 to 10, a 13!! 
 
That worry expressed, I am however glad I stumbled across this because I now am going to make a system image of my drive before upgrading.  Probably a good practice anywho.....

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.