I have a project that's mainly MIDI but has some audio clips as well. While Sonar was closed I deleted one of these clips from my hard drive, and naturally Sonar warned me about the missing audio when I next loaded the project. Of course I just clicked "skip." 
 
Now when I load the project, Sonar is telling me that all of the other audio clips are missing too. Of course they're all there, so it must be a bug. It worries me when I'm working on a project and little corruptions like this start to appear...I worry about what's going to go wrong next....I mean it's a minor inconvenience to have to close the warning dialog every time I open the project but still....this is just like another problem I have with a lot of projects, whereby upon opening them Sonar tells me that certain synths are going to silent outputs even though they're not. And I have to click the dialog away every time I open the project, and also when I close the preference window. I think Sonar has some issues with warning dialogs in that it doesn't know when to stop giving them sometimes....anyone else? 

can you restore the deleted file from the recycle bin?
 
then create a new folder and copy your project file and the audio folder into this new folder.
 
try opening the copy of the project in the new folder and see if things are working.
 

Just a couple of thoughts:
 
1.  I did the same thing to myself the other day.  I chose to fix it by just creating a new project, then imported only the actual clips I intended to have present, and that took care of it.
 
2.  I don't know if this would work, but what would happen if you created a new clip with the name of the missing one?  Would that make the error go away?
 
Anyways, option 1 worked for me.  Good luck, 
 
Bob Bone
 

Maybe this is relevant? 
 A quote from Skook on a post of mine.
"It appears that once the "silent hardware" condition occurs in a project, the error flag is set and is never reset. I know of no way to manually reset the error flag in the project. There is a way to suppress the error message from ever popping up. To suppress the error message set WarnSilentBuses to 0 (zero) in Edit > Preferences > File > Initialization File. As with all advanced settings make sure the Advanced radio button is selected at the bottom of the Preferences dialog to see the Initialization File option."
 

If the remaining clips are nondestructive edits of the wav you deleted (i.e. Not bounced) sonar won't like it
Hth

Maybe this is relevant? 
 A quote from Skook on a post of mine.
"It appears that once the "silent hardware" condition occurs in a project, the error flag is set and is never reset. I know of no way to manually reset the error flag in the project. There is a way to suppress the error message from ever popping up. To suppress the error message set WarnSilentBuses to 0 (zero) in Edit > Preferences > File > Initialization File. As with all advanced settings make sure the Advanced radio button is selected at the bottom of the Preferences dialog to see the Initialization File option."
 
Thanks GLENN (and SCOOK) - I was getting the SILENT BUS error message and it was driving me mad!