As other posters have mentioned, I'm betting on operator error. That fact that TV Shows directories were deleted, but Movies directories were not deleted, would seem to indicate that the links to those directories were not treated the same - even though the OP says they were.
I have moved Jails twice since running FreeNAS 9. The first time I did it, I tried using the CLI to save time and managed to delete all my data by mistake. Nowadays, I know why this happened - it's an easy mistake to make when one is not familiar with the operating system. Since I keep good backups, it was annoying but it was not a crisis.
The second time I moved my jails, I worked mostly through the GUI. First, I removed the links to the data. Then I backed up the metadata and configuration files for my plugins (this I had to do through the CLI.) Then I deleted the plugins and the jails (using the GUI.) Next, I reinstalled the plugins on another volume (using the GUI,) then restored the metadata and configurations (using the CLI,) then redefined the links to the data (using the GUI.) Everything went fine.
Some things I have learned:
1) Moving jails is not a trivial task. There are lots of ways to mess things up.
2) Make backups of your plugin configurations and metadata. I do this now, as a regular part of my system maintenance.