This is strange.
After the last rejection due to iPad 3 compatibility issues, we uploaded a new binary to Apple and made some changes to the content of the folio that was regarded as "objectionable" which consisted of a complete article and an image in the TOC article.
After updating the folio, the article was removed, but the TOC article didn't update and was left as is with the problematic photo that caused the rejection.
After achiving and downloading again, the correct content appeared.
What's going on here?