Is there any way to undo whatever Plex has done to my media files

I had installed and configured Plex on my Synology NAS DS1515+ yesterday, but I had no idea that if I select the features like Metadata, sync, etc etc on the PLEX setup I will end up doubling the size of each and every media file be it music, video etc.
Plex has eaten up almost 4TB of disc space from my NAS and now I have run out of space.
I stopped all that was going on with Plex application and deleted the Plex account and the Plex Home Directory as well but cannot free up disc space.
Is there any way to undo what ever Plex has done......
PLEASE HELP............