Weird problem with cleaning directory

I'm a frequent project directory cleaner. However, I'm having an issue with a current project where, when I go to clean it and the project directory window comes up, it says "276 out of 292 files are not being used". This seems wrong to me, as the song so far is 40+ tracks and over a half hour long. There should be considerably more than 16 files being used in the directory. So now I'm not cleaning this project's directory because I'm afraid of losing a ton of WAVs. I've checked my media path in Project Settings and it indeed leads to that same folder which is, I assume, the folder Reaper grabs all the WAVs from when I boot the project... Anyone here have any ideas what might be going on?

You can get the accurate answer and the best solution from the person who have cleaning business or company, i haven't any hard and fast knowledge about this !

Why nSo you are not saving to a project specific location? This can get you in a mess. Check out the reaper 101 on reaperblog to get your projects set up in their own folders. That makes it much easier to know what files a project is using.

I have had bits go missing in the past when cleaning project directories and put it down to me making a silly mistake. However, since the last one (well over a year ago) I clean up via explorer by cutting out all the undo's. baks and all the old .RPPs's and put them on an external drive. I then use the 'Clean current project directory' option in Reaper after emptying the recycle bin and cutting them over to the external drive. If a file comes up missing I point Reaper to the external drive. As it is all individual files in date order I can clean this ext drive every six months or so. This may seem a bit OTT but works for me pretty much like a back up. Haven't had to test it yet :).

It's non-destructive editing of WAV files and midi files are embedded in the project. Meaning it's possible there aren't as many files as it appears. However, a good test to answer it for you would be to Save As and check "Copy files" and "Create Subdirectory" to some other folder. Then open that project and make sure it is OK. If so, delete the previous one. That's not what you always need to do but will/should answer the question you are rightfully asking at the moment.