I don't think you should have ANY unit with no faction owning it. Why don't you just delete the whole entry in the file, rather than just removing the ownership. What you are creating is a piece of data which the game engine WILL read, only missing a key piece of data.
Also, if you remove part of a reference, in one file, show_err should help to tell you wher it got upset.
To use show_err, go to your RTW shortcut, and add show_err at the end of the command line.
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