Try loading it using the Sony Library. Calibre does not paginate before loading, the SL does. It could be it's taking 'too long' to repaginate when you change the font size - how long are you waiting before reset? I've had some long books take as much as five minutes to reformat.
If you 'corrupted' the file on the Reader, the file on your computer would still be the same as it was before.
So either reload with the SL, or try being more patient.
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