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Why use PDF files on the iPad if you already have ePub ones? For ePub files you can use either the Apple provided iBooks reader, or the independent Stanza reader. EPub files are far better as they support reflowable text so that it is easy to set font sizes to suit you.
To get rid of a particular format you can select all the books and select Edit Metadata. One of the options offered on the resulting dialog is to remove selected formats.
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