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Also I checked in jrunscript under these circumstances that the code called by Util.resolveSymlink would work, as would the call to Util.deleteFile.
In the case of tdtappe, running Java 6, resolveSymlink would be expected to fail, explaining the skipping deletion of directory … message. This I could fix by just trying deleteFile anyway—if it is really a symlink to a directory, that will work, but if it is really a directory, it should fail because the directory is not empty. It makes me a little nervous because isDirectory would also be true for a real directory created by 1.597+ (or a partly successful earlier migration), and relying on File.delete to fail in this case seems dangerous.
In the case of Steve Haworth, running Java 8, I am puzzled. I see no FINE-level messages here so I assume you did not turn on the custom logger, which might have some crucial information.