48k project actually has all 96k samples MOTU 24 IO Sonar x1

What has happened is that you have recorded 96k audio into a 48k session, (as you have figured out) do to your interface being locked to 96k. As far as sonar is concerned it thinks the audio is 48k & has most likely given the .wav files 48k headers. 
What you need to do is SRC (sample rate convert) the 96k source audio to match your 48k session rate.
Your next hurdle is to find a SRC program that will let you specify the source & destination rates. Pro Tools or SoX come to mind 1st. You will need to tell the SRC software that the audio is actually 96k & that you want it to be 48k. Most DAW's won't let you do this. Once converted replace the source audio with the SRC'd files & re-open the sonar session.
 

also - checking the source file from the import dialog box, they all say 96k, is there a way to fool sonar into thinking it's a 96k project?

If you end up needing to play around with changing headers or SRCing It's hard to beat SoX. You can download the code from this http://sourceforge.net/projects/sox/
 
After installation copy these batch files I created into the SoX directory. header-fix-batch.zip
 

• Create a directory called fixed at the root of your c drive "c:\fixed"
• Drag & Drop your source audio files that need to be fixed onto the appropriate batch file.
• Replace the source files with the "fixed" files from the "fixed" folder

 
The nice thing about this method it that it is completely loss-less, no SRCing only file playback rate changing.

One thing to note. If your motu is now clocked correctly @ 48k, your "messed up" 48k session should sound 1/2 speed if the audio is actually 96.
Sonar bases it project rate on the audio file/header content. 
If all of your project audio files are 96k with fixed/correct 96k header information the session rate will change & say 96k regardless of what the Sonar preferences are set to.

Tom Riggs
Create a new project at 96 and import the audio files. Do not delete the clips in the existing project as it could also delete the source audio files.

For the record, this is not accurate. SONAR will never delete an audio file except when the clips representing them are deleted in the same session in which they were recorded before saving. That said, I always recommend working with a copy of the project in its own folder with copied audio when doing anything tricky like this.
 
Creating a new project from scratch might not be practical if it's already far along in the mixing process with advanced routing and FX in place and tweaked.