That's the thing, I didn't, it just blanked it itself. Perhaps it became corrupt and it did the job and then trying to access the music that was no longer there may have added the folders? I'm not sure.
I just know that it was a stick full of music in their own directories that, for whatever reason, it just decided to delete or quick format and then, when I checked the stick, a new android folder had been added with a couple of sub folders and a couple of music related index files, was also the standard android .nomedia file in at least one sub directory so it was set up as an android system storage drive.
I just added some music folders back to the root of the stick, alongside the android folder rather than inside it and checked it worked okay then found that the shuffle and restart issues seem to have also been fixed.