Apparently I've tweaked something that I should not have, so here I am, groveling and sniveling for help.
 
In Preferences, there's an option under File/Audio Data to Always Copy Imported Audio Files. Every song I work on has its own folder, and beneath that is an audio folder, where all the data is stored. Typically, after I'm all done, I'll open this up in Windows Explorer WITH THE SONG OPENED UP IN X3, highlight all files, and hit Delete. A warning always pops up that certain files are in use (in Sonar). Pressing Skip results in deleting the files NOT IN USE by Sonar, resulting in a cleaner directory. IOW, only those files required for the song stay.
 
Now, for some reason, when I carry out the above action, ALL the files get deleted, even though they are "in use" by Sonar. To verify, I went back to a tune I did months ago, and it works like a charm (only unused files get deleted).
 
So, what did I click that should've been left alone?

I see you like to live dangerously...
 
To slim down a finished project, "Save As" to a different folder, and check BOTH "Copy all Audio with Project" AND "Create One File Per Clip." The new folder will contain only audio used in that project.

I have to say - I would never ever think to do that in a project - creative, but inherently unsafe.
 
I do precisely as Craig has posted, and it keeps projects nice and cleaned up, by getting to the same point of ending up with only audio clips that are actually used in the project, but since it is a copy process, I am in no danger of losing any audio that I am actively referencing in the project.
 
I hope that helps, 
 
Bob Bone
 

I don't know what you've changed... but it seems likely that if SONAR has reliably warned you about "files in use" in the past, then for this new project, the files in the project are still in use, but they are not the ones you're looking at in Windows Explorer... I would follow Craig's advice - it's what I do myself.
 
Let me add my voice to the "you do what??!!!??!" sentiment. That just can't be a safe way of operating.

Though I agree with everyone else, I don't think his method is that unsafe. Next time he opens the project he can just see if SONAR misses anything, and then yank it back out of the recycle bin. As long as doesn't "take out the trash" before double-checking he'll be fine.  the only time I empty my recycle bin is when I run CCleaner or notice space is getting scarce.
 

I expect that it is Windows rather than Sonar that issues the files in use warning. The problem is that windows will generally only refuse to delete or move a file that is actually open and in use by a program. While Sonar may produce a lot of files associated with a project, that it knows are part of the project, they are not all necessarily open as far as windows is concerned just because a project is open. Sonar knows to save such files from within Sonar, but Windows does not have a clue that the files, once closed, belong to Sonar, let alone to a particular project.

...wicked
Though I agree with everyone else, I don't think his method is that unsafe. Next time he opens the project he can just see if SONAR misses anything, and then yank it back out of the recycle bin. As long as doesn't "take out the trash" before double-checking he'll be fine.

That seems a lot more complicated than "save as" and checking two boxes 

But why would you ever choose to deliberately put yourself in the position of HAVING to potentially pull files out of the Trash?
 
Regardless of whether or not the mechanics of the built-in deletion protections probably insulate you from actually deleting needed/active clips, and regardless of them being saved for you by Windows in the Trash folder, it is in my opinion a faulty way of thinking.  
 
The fact that for WHATEVER reason, the original poster's active audio clips seem to have been deleted is PRECISELY why I would never put myself in that position in the first place.
 
I would HOPE that the philosophy of "never delete things you need" would 'win' in any kind of cranial debate you might be having.
 
It's a big planet, and you can certainly do as you choose, so have at it in any manner that makes sense to you.  
 
Myself, I would forever NEVER ever clean out audio in the manner chosen by the original poster.
 
Bob Bone
 

I wouldn't either, but it's not terribly different than I do with other procedures. For example, I had and then dumped JBridge, but despite best uninstalling methods it left a slew of bridged plugs and data files. So I moved them all over to a temporary folder I called "_DELETE Jbridge plugz" and then went about my business, figuring if SONAR coughed up a "can't find..." dialog I'd just copy over whatever it was.
 
In fact, I still have a "VST Plugins" folder from my last DAW. If i open an old project and it can't find something weird I check there first and so far so good, the random VST is always in there. This is of course part of my GAS/VST DAWSlim Program (tm) 
 
Granted, the Save As is the best way, though a little labor intensive. I still use that over the CWAF, which frankly scares the crap out of me as I once had it miss a whole bunch of files. But hey, I've been clamoring for more elegant asset mgmt for some time now. 
 
 

slartabartfast
I expect that it is Windows rather than Sonar that issues the files in use warning. The problem is that windows will generally only refuse to delete or move a file that is actually open and in use by a program. While Sonar may produce a lot of files associated with a project, that it knows are part of the project, they are not all necessarily open as far as windows is concerned just because a project is open. Sonar knows to save such files from within Sonar, but Windows does not have a clue that the files, once closed, belong to Sonar, let alone to a particular project.

This is exactly what I was about to type before seeing the above-quoted post. You cannot assume that every file associated with a SONAR project is open from Windows' perspective.