So, I've come to realize the complexity of where your project is set to 44.1Khz, but your A/D converter is set to 96Khz, recording audio. Granted, this is a bad idea, because they are simply different. However, Sonar plays back the audio just fine. The problem comes in when the Export occurs. Sometimes the Exported playback is slow or fast (high/low pitched) because of the mis-matched sampling rate. 
 
I've been working diligently to fix this problem in a client's session, including resampling in Wavelab, and editing the .wav header sampling rate and re-import into Sonar (didn't work in this case). Here, the sampling rate of the A/D was changed for the overdubs to a different, higher rate even though the project's sampling rate setting never changed. The only real fix I can find is to "play" the audio from Sonar out a D/A and resample the audio fresh into an A/D to another machine.
 
Feature Request #1: Export "as-played" checkbox.


When you export a track or Entire Mix, the DAW would export (dither or no dither) at the played back sampling rate, (even if it has to convert it using a couple of plug-in type engines to sort of "re-write" the samples as a newly (but with zero added analog noise)). However, doing it this way never requires the audio to leave the DAW. It's like doing what I'm resorting to above, but inside Sonar.
The idea is, if Sonar plays back the audio correctly, I'd like to Export the audio "as-is", or "as-played" to a new .wav file, to ensure it plays back the same way in Windows Media Player, or Wavelab, for example.
 
Feature Request #2: Resample clip.
 
I'm sure I'm not the first to request this, but even Wavelab's re-sample doesn't do what you'd hope. Here, re-sampling could be done as other DAW's do it, but with the added feature above, to play back the audio through a "plug-in" type engine, and resample the audio as a whole new analog input--only it never leaves the DAW. Yes, you can export and re-import into a new project, but that's seriously a lot of work.
 
If there's already a way to do this, please let me know, but I haven't found it yet. Thanks!!

UPDATE
So, thanks to some other members, I was able to fix my situation:
 
Scenario
Project set to 44.1Khz, but the A/D sampled the audio at 96Khz, and Sonar would playback the audio at its sampled rate, not the project rate, it seems. However, when exporting, Sonar will export at the project rate, so the audio plays back way slower. 

My solution (as suggested by other members)
1) Back up the project and Bounce all clips with Bounce to Clips. This simplifies the number of clips to correct, and separates them by name, potentially.
2) Delete all clips and save the resulting project a as template. Close the project, but obviously don't overwrite your previous project.
3) Open the template with a Default Sampling Rate of 96khz. Set this in Preferences. 
4) Use the Header Investigator.exe to open all the bounced clips from Step 1.
5) In Header Investigator, Highlight all the clips in question. Uncheck all boxes except for sampling rate. Change the rate to 96000Hz and apply the change. If you receive an error, be sure these files aren't opened up somewhere else.
6) Back in the template from Step 3, verify the project is set to 96Khz and import the clips you changed.
 
Now, when the Export is done, it will likely play correctly.

Sidenote: Wavelab just released Pro 9, which comes with a re-sampling plug-in. Had I not been able to fix my problem aside from D/A-A/D the audio, this would have been a great fix. CW needs that plug-in, or one like it to be part of Sonar.  

My goodness what an undertaking.
 
May I ask - is it the Motu that force you to set a fixed rate to 96k, or?
Using ASIO?
Or some setting letting Sonar run soundcard exclusive would allow to set to 44k if running project in that rate?
 
Just never had to work like that with RME stuff.
Whatever rate a daw uses in ASIO also sets soundcard to that rate.
Even other apps running ASIO changes soundcard setting until next app use something else.
 
But other drivers like DirectSound and similar usually let soundcard resample to whatever setting it has.
Don't remember about WDM how those drivers work for RME.

Nah, it was accidental that the MOTU was set to 96kHz and the Project was at 44.1kHz. However, Sonar gives a false impression of how the audio plays. Recently, there was a change in Sonar that allows multiple different sampling and bit rate clips to play in Sonar (if I read that correctly). What I'm finding is that Sonar plays black the audio at the sampling rates of the clips, not the project, but it Exports the audio at the sampling rate of the project, not the clips.
 
At least, this is my experience. For example, I have clips sampled at 96kHz in a 44.1kHz project. When you hit play on the Sonar transport, the audio plays back just fine. However, when you export the audio and open the resulting audio in another program, it's SUPER slow. 

I had similar issues with Sonar and when Windows Sounds was active - like playing back a windows sound when a dialog pops up and similar could reset soundcard samplerate to 44k even though Sonar project was running 48k, and speed of playback was altered.
 
So I turned off Windows Sound since then, to never interfere and playing sounds for different events.
 
I also at times had issues running a daw when I had Windows have any audio devices that are assigned to the same as the daw - this to have ability to run MediaPlayer and similar. But changed to use Foobar2000 which also has a ASIO plugin and don't need Windows audio assigned drivers. So to play back rendered audio and check out final quality FB2000 is run instead.
 
Hope you get some new ideas how to proceed...