I have just found this thread looking for a similar answer, so to confirm in 2018…
My situation, I created several new projects at the same time (coping files from a big recording session in one project). I had started recording on track 3 and realised afterwards all my files were going in to project 1 audio folder. I can see in the pool window the “project folder” which is unable to be changed (set to track 1/audio).
So to confirm, currently on version 9 you can’t change the project folder. (not sure if this differs on 9.5 onwards).
I did find this help article, but all this did was create a folder inside the audio folder of the wrong project (ie track 1/audio/newfolder/):
So, to confirm, I tried the advice above in this thread. saved my project, created a new folder “track 3 V2” and backed up the project to that folder, deselecting “keep current project active” and making sure the files were copied over. Afterwards, I closed the current project and opened the new one and it worked like a treat. I could also see the files had copied into the new folder and most important…
The new project was using the new project folder in the pool window.
Hope that clears up some of the answers above.