I have a java application which splits a pdf into sections using itext, then stitches a selection of these up together again. The original pdf has many embedded fonts varying in type (all non-system fonts). When I stitch the pdf's up again, some of the embedded fonts are missing.
For example, this is a clipping from the original fonts list:

This is a clipping from the generated pdf font list:

I am using PdfWriter and PdfReader to copy the pages into the new document, with PdfContent and addTemplate().
PdfImportedPage. I suspect if you looked at a page-by-page breakdown of font usage, you'll find that they're correct. - Mark Storer