Yes you can use split mode when using HTML5. We typically recommend using a tool like pdftk to split your document into individual pages. You also need to supply a JSON file when you do this. The JSON file is typically created using PDF2JSON.
The following example splits a pdf file into individual pages:
pdftk "Paper.pdf" burst output "Paper_%1d.pdf" compress
Create the JSON file using PDF2JSON in the following way:
pdf2json "Paper.pdf" -enc UTF-8 -compress -split 10 "Paper.pdf_%.js"
Then supply the PDF file and the JSON file in the following format to FlexPaper:
PDFFile : "Paper_[*,2].pdf",
JSONFile : 'Paper.pdf_{page}.js',