So apparently the decoder object created by Encode::Guess remembers that it's UTF-16 but forgets immediately whether it was big-endian or little-endian? That seems broken.
Looking at the code, it "forgets" if it finds a BOM, it remembers otherwise. That's reasonable since it would cause $enc->encode to add the BOM if and only if there was one present in the sample.
You should probably incorporate into your code the couple of lines of E::G you actually do use. Then , you can change this behaviour if you don't like it.
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