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I don't know if there is any Calibre-specific metadata that would be overwritten by the Sony software, but I suspect that there might be some. I would create a new library folder, do the pagination bit in Sony, and then re-import back into Calibre. You might lose tags, but if you don't use them that would be cleaner.
Also, I have switched to EPUB from LRF for all new books because the pagination and the rendering is so much faster, not to mention that changing font sizes is much quicker with EPUB.
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