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You can specify the encoding when using mobigen. I haven't bothered with getting the filepos exactly right since it's not that critical. As long as you make sure you dont insert an anchor inside another <> you're fine.
If I had to guess I'd say filepos represents byte position not character position, since in the cp1252 encoding every character is one byte and that was the original encoding mobigen used, back when it was prcgen.
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