I just found a section talking about "Defragmenting a Project". In it it says you can make sure a project's data is all in one place (for quick read times) by saving it as a bundle, unbundling it and then saving it again normally. Most of the system performance improvements section (as well as other parts of the manual) seem to be very old so the Per Project Folders thing may not have been added at the time of writing.
I am wondering if perhaps using the Save As/PPAF/Copy All Audio function and saving it to a new place will have the same affect (as in gathering up all the scattered bits of the project on the drive and then saving them in a nice tidy hunk of disk space). Seems like it might but I'm wondering if anyone knows for sure. I find Bundles are a sure fire way to get a project to start acting quirky so I try to avoid them and if the goal is to make a project work BETTER seems like a "1 step forward 2 steps back" type of "fix".
The entry appears on page 1462 of the Reference Guide:
"Your project file may be excessively fragmented
Audio data can be processed most efficiently if it is arranged in consecutive physical locations on your hard drive.
During normal SONAR usage, a project's audio data can become fragmented into chunks stored at discontiguous locations on your disk. Accessing these discontiguous chunks can consume extra processing time, which can leadto dropouts.
Try defragmenting your project file:
1. Open the project file that has audio problems.
2. Save it as a Cakewalk Bundle (.cwb) file by selecting Save As from the File menu and selecting Cakewalk
Bundle from the Save As Type drop-down list and clicking the Save button.
3. Close the project.
4. Open the Cakewalk Bundle you just closedSaving then re-opening the bundle file automatically defragments the audio data used by the project, reducing the chances of a dropout or other audio problem.
When you are ready to save the file again, you may want to save it as a normal (.cwp) file. Saving and opening .cwp files takes less time than saving and opening bundle files."
Cheers.