Am I ever going to be able to clean up my audio folders?

the CWAF tool is a better option for batch clean up.
I how ever do use the clean audio folders tool quite often and it takes for ever and a life time but it does in deed work.
 
get in to the habit of good house cleaning while projects are in progress. rather then letting a slew of them pile up.
after you complete all tracks for example, bounce to clips all your tracks, then use the Clean audio folder tool.
I started doing this a few years ago and it is a G Send. I like to be organized and find files within folders so all named tracks in folders are there.
 
the downside is, I don't have little clips to choose from. but I don't consider that a downside to be honest. if I need an audio clip, its typically the whole clip, not just the bridge or chorus of that clip.
if you need to save clips within a track, copy those a side, than bounce all your tracks to clips.
it really does make a huge differential.

OK a couple follow up questions...
 
1) I am not certain, but I suspect that some of the files in my root "Cakewalk Projects" and my "Audio Data" folder are the same files that somehow at some point just got copied. Maybe not all, but definitely at least some. Do you think I'd run into problems if I drag moved them all to the same "Audio Data" folder and chose to skip the ones it finds and then compare/delete the ones that were in both?
 
2) When working with the CWAF tool, I think my biggest problem is that lets say I have "Song 1" then "Song 1 (Version 2)" and "Song 1 (Version 3)".... If I just go to "Song 1 (Version 3)" and bounce lets say the lead singers vocals all to one clip so it cuts down on the amount of audio files needed for that project, they're still going to be all split up in the first and second versions, right? Seems like the only way to make that tool effective is to give in and delete all older versions of project files... Is that right?
 
3) Base57's suggestion is something I had never heard of before... I had never tried the Consolidate Project Audio command before... That is really interesting in that I can kind of wrap my head around that... so if I did that for every projects (at least starting with the important ones)... In theory I could do that for every song and make it like as if I had been doing Per-Project Audio folders from the beginning... And then I can delete the big catch all "Audio Data" folder because I've made copis of any audio that would have been in there anyway by using the Consolidate Project Audio command on a million different projects haha.
 
It's a huge job but that's an interestingly new way of looking at it...

Do you really need all those 500 projects? Couldn't you take, say, the twenty most relevant ones and fix those in one of the ways described above?

Then if you're still insecure, backup the remaining projects and both audio folders to an external disk and forget about them.

25 or 50 or 100 gigs of messy storage is nothing to worry about. 
 
My self I would put the whole thing on a data drive and forget about it. This is more or less what happens to older files I have.  Then one day if I decide I want to re do that project, I just browse and open and then use "save as" with copy audio and save to my working drive. The old copy remains as a back up and the new copy starts fresh in my uncluttered storage space. 

This would be a nice feature request. A batch function that could drill into a select folder (especially the global audio one), then run a "save as" on ALL .wrk, .cwp files to auto name a new folder with the project file name to comply with the current per project folder layout. If already existing, would need to prompt the user for an overwrite or not. This has application now since "new project" without choosing a project name dumps everything into the global audio until a save is performed (and then only copies AFAICT).