Protecting Audio Files

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 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
 

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.
 

...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 

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. 
 
 

Thanks for all the advice. I know that my method of cleaning up stuff is a bit dangerous, and I've got plenty of old battle scars from Windows to tread carefully.
 
I think the issue has something to do with the template I made. Prior to this, I didn't use a template, then got tired of doing the same old setup routine. Oh, well. I'm playing safe as a result. No more blind deletions.