I often get queries from Correspondents regarding the inability of some AppleScripts (and some of my shareware apps which are AppleScript based) to access files when File Vault is activated. Does "Finder got an error: Can't get name of alias "your_disk_path" number -1728" look familiar? The trouble is that File Vault encrypts your "home" directory. AppleScript cannot penetrate File Vault so you will get an error when you run an AppleScript that attempts to access any files in the home directory. There's no way around this. Isn't that a good thing? However, I suppose that there may be a way of catching the error before the script tries to run; but even so, if you are using File Vault and you are getting errors from AppleScripts, could you just turn File Vault off for a bit while the script needs to work? I dunno. Seems to me you only want File Vault operative when you are not around. Maybe that's a Whole 'Nother AppleScript. I have never used File Vault so I don't know.
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