I stopped using Templates a while ago when I discovered something that works better for me.
Blank CWP files. Or I'll do the same as above and just start a new Project and use track templates to populate it.
I create a blank project with all the pre meditated stuff, and save it as a CWP file. I then open it and re save using "per project" and "save audio with project" naming the songs.
Note you should always "save as" before you hit the record button or the audio will be stored in the original folder. Not a big deal as it will get copied & moved once you do the save as, But now you have unwanted audio in the templates folder.
I never use the opening dialog box, I told it to go away. I just open from the file menu.
OP- I sure hope you have a back up of all that ?
I would dump the whole works to a data drive - twice even
If you truly have made the mistake of keeping all your audio in one global audio folder
then you will need to clean things up using "SAVE AS"
Back everything up.
Using Widows Explorer make a new Sonar Projects master folder(s) somewhere. I use the root of a DATA drive and make folders for each album or type of project like Backing tracks, Song idea's.
Then in Sonar
Select "use per project folders" in preferences first.
Open each project and then use SAVE AS to direct the song to the new sonar projects folder.
Make sure to check "copy all audio with project"
This will make a clean copy and only save the audio needed.
When done you can now safely delete the original global audio folders contents.