Pages Missing During Export as PDF

I've been working on a long document in InDesign. It is a book that is comprised of about +200 documents. Each of these documents includes photos and text, along with a header and summary paragraph style. These paragraph styles are used to create a table of contents. The table of contents gives me the correct page numbers for each of the files, but when I export the PDF, after a certain chapter, the table of contents no longer links directly to those articles. It appears that 1-2 pages is missing from each of the documents after a certain document. I only have 1 layer, I have used the same 1 master slide for each document. I originally created the document using 1 default style and then re-saving that file as different file names as each document was created. The end result is that the page count for the document at the bottom corner is in the neighborhood of 1200 pages but the actual PDF file is only 1016 pages.
Any suggestions on how to fix this? I have absolutely no clue where to look for a solution. (As per Adobe's customer support, I did remove a folder in the App Data section)
Edit: I forgot to include; when I export the individual documents to PDF that have missing pages, they export without missing pages. The issue only happens when exporting the documents as a book.
Message was edited by: ccarline711

Hi Lukas
You can quickly test this by creating a document with bit of text. Then move (you don't want to delete it) the selected font away from system's font repository. When you open the document again, you will be warned about the missing font.
So InDesign already does checkings for you. The default Export tool also checks for missing fonts for you. If you are doing a custome export, you might need to implement your own.

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