Some epub formatting and specified fonts are lost after uploading epub to iTunes U and then opening it in iBooks

I have been using DropBox to test my epub in ibooks and just recently uploaded the epub to iTunes U because the file size was getting so big because of the videos for the course that DropBox could no longer open it. My "com.apple.ibooks.display-options.xml" file (specifying to use Helvetica) inside of the "META-INF" has been working all along while I have been using DropBox to open it in iBooks. But ever since I uploaded the same epub file to iTunes U and opened the book in iBooks, the font doesn't show up as Helvetica anymore and my paragraph styles are also being ignored. I checked my css files and made sure they all said Helvetica, because my formatting for my tables is the only thing now showing Helvetica. After I unzip and make my edits to the css etc. and rezip and upload to iTunes U, does iTunes U ignore or overwrite files you have changed inside of your epub?
This worries me that iTunes U seems to be having problems with this, and it makes me wonder if I am going about this wrong?
My file size is 129.2 MB and I still have some videos to add to the course. FYI I am creating this epub for the iPhone because we already have a version with iBooks Author for the iPad, but iBA doesn't allow it to open on the iPhone.
Any help or advice would be much appreciated!

What is the name of your private site?
-Thanks

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