Hey Chris,
I’m a little confused, are you using the Split Document option for the Chapter title or whatever starts each chapter and you’re getting this issue? or are you applying the Split Document option for the endnotes? or for a paragraph style after a footnote? I only ask because your post sounds like you are applying it to footnotes. And are you using the Split Document option on styles within your chapter/section? I would advise against that as InDesign will view that as the end of the chapter/section and all the footnotes/endnotes will be placed at the end of each (you are basically telling InDesign to create a new HTML page every time you use Split Document and theoretically each chapter should be in one HTML page not multiple, if you’re doing coding after export, you can get around this but its a lot easier just to do it in InDesign) and really unless you have an image you want to force to another page, I would advise against using the Split Document option on any style other than the first style at the start of each chapter (usually the chapter number or title).
You don’t need to abandon your endnotes, that’s actually rather normal, unless you are taking advantage of the popup notes in iBooks, endnotes are really the only way to do footnotes.
Hopefully that made sense, let me know if you have more questions,
Aaron