BD's support of Unicode seems spotty in my experience.
What you need to do is to download the referenced free font from Berkley and install it on your computer. Then under either calbrie or BD reference the font as the one used in the book. The font can be redistributed free. The native fonts in the Sony Reader will not support the Latin/Greek glyph coding scheme.
For splitting larger books into smaller volumes I have always used an external text editor such as UltraEdit. This is much faster and easier than messing with it in BD.
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