By changing the default to 24/96 I can switch between projects without this problem.  So I guess the bug here is inability to switch between different rates without dropping outputs??  
 
It turns out those busses were not the only problem, other channels were reset to different inputs without warning or fanfare.
 

You need to set the bit depth in two places in Sonar. First is Driver settings under audio. The second is in Audio Data under File.
 
 

200bpm
By changing the default to 24/96 I can switch between projects without this problem.  So I guess the bug here is inability to switch between different rates without dropping outputs??  

Yes, I think that the problem is related to the control of your interface and the switching of it from one sample rate to another. Something is blocking the switch between the Sample Rates. On my computer, in the system tray at the bottom right, there is an RME Driver Icon you can open to see what RME reports the current Sample Rate to be. Be warned, having this open may block Sonar from changing the rate. This is what I was describing with RME DigiCheck (which you should download if you haven't).
http://www.rme-audio.de/en_downloads.php?page=content/downloads/en_downloads_driver&subpage=content/downloads/en_downloads_digicheck
 
So, something is blocking Sonar for making the switch on your computer. I'm not positive what it is. When Sonar detects that there is no ASIO Interface matching the project, it is clearing your stuff out. That's your prob. So, what is blocking Sonar from altering it. That's why I kept asking about ASIO. I was wondering if a wrong driver setting might block it. Having another sound program open locking the device would do it too. That was what @ was trying to tell you.
 
Do you follow the problem? Ask if you are confused. It's a confusing concept. Basically, at one moment, Sonar recognizes a device at 96 it can use, and then at the next moment it doesn't.
 
Again, I'm travelling and have only Linux with me. When I'm home I'll test with Sonar. It's possible that the 44.1 project you open somehow isn't all the way closed or for some reason hasn't released your device.
 
Here's another thing to try (something I might do),
1. Open your 96 Proj. - don't close it
2. Create your 44.1 Proj. - don't close it
3. (Without closing either project) Alt+W and choose to switch between the projects. Switch back
 
How does that work? Watch your Device. Is it smoothly changing between 96 and 44.1?
 
I'm not positive if you will accidentally lock your device by having that RME Driver window open from the system tray or not. You'll have to try it.

200bpm
****ed sonar forum still won't let me attach image.  YOu will have to use your imagination.

Use www.imgur.com. It's not difficult. 

When Sonar doesn't see an interface at the right Sample Rate and it cannot alter the rate to the correct rate, it basically behaves similarly to how it behaves when the interface is off.

200bpm
I dont give any extra respect, consideration, or fealty to anyone based on post count or "reputation"; either help or don't help.

 
People can't help without a coherent description of the problem. The definition for "dropping outputs" exists only in your lexicon; the information you have provided in the last few posts should have been in the first post as it defines what you mean by "dropping outputs." This is not about correcting syntax or spelling, but transfer of useful information in the quest to find a solution.

BTW, you mentioned rolling back your RME Driver. I'm on the latest RME USB Driver and DigiCheck on all the computers I use with my UCX - Except for Linux where I have to use it in CC mode.

I can only speak for my interface, but it is probably similar. It is highly recommended for my interface to close any applications in use prior to any sampling adjustments (done via the ASIO panel). However, I tend to blow this off all the time, as my drivers will handshake with X3 and adjust. At times, this will cause the audio engine to drop out (rare) which I simply re-enable in the control bar (I noticed yours dropped out too). As I am not sure of the sampling rate in a project, I am grateful for this handshaking (which can be undermined if multiple applications are accessing the interface, especially Windows). It seems that your interface appears as a different output to X3 with different sampling rates (not sure here), so when the sample rates do not match it is giving you that warning (i.e. X3 expects to be talking to a 16/96 interface and isn't seeing one).
 
Ideally, applications should be closed, interface adjusted, and then X3 re-opened. The default for new projects can be specified in preferences within X3 (I would set these for what you have traditionally worked in, and be sure the interface is set there via its GUI as well). If you are running ASIO mode, you can only access buffers within X3 via the "ASIO panel" button, which launches the interface GUI.
 
I hope this helps.

Craig,
In the first post, I linked exactly the problem I was having.  You're trying to seem smart but failed at basic reading comprehension.

Please be considerate of others and take feedback constructively. People taking the time to try to help (even if they fail) is a privilege and not a right.