Thanks for responding. I had a look at the link you provided and the suggestion to use a hidden file to stop deletion, however Filebot still deleted the folder when I tried that.

When I use rename on TV shows (haven't tested movies) my format also moves the file to the correct location. Since 4.7 Filebot is deleting the original folder. The files are being moved from E:/Download/Completed and the expression I am using is E:/TV/{n}/{'Season '+s.pad(2)}/{n} - {s00e00} - {t ...