I have been changing font sizes on epubs I purchased from SONY's store regularly and this has never happened to me - although at times it would do weird things at the 'next page' line - like adding extra empty lines. But it has generally to do with poor epub formatting.
But I have never seen anything like what you describe.
I would assume it has something to do with poor formatting of the epub.
A PDF would indeed behave that way.
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