Mostly back as it was.
The infinite Shared folders have been caused by my numerous attempts to get Plex to find my data, I think. There was a "create directory" tick box somewhere and along the way that I left ticked knowing the folder already existed. My music folder was also in three different places, I have a sonos network speaker. I had similar difficulties getting it to work and kept making changes one at a time to try and get it to work.
Even after all that I don't understand why this would result in files being copied. I was under the impression that the data only has to reside in one place and I'm only telling different programs where to look?
When deleting my duplicate files I have ended up with some I can't delete because they are "open in another program", I don't have any of these files open. How do I find out in FreeNAS what is using them?
Anyway time to get Plex and my Sonos speaker working again, carefully and slowly this time!
As wonderful as FreeNAS is, it is all too easy to tie yourself in knots by "trying" different settings without really knowing what you are doing, back to the book!