No matter how many chapters you have in your document, and how long they are, you can convert it to EPUB with Atlantis Word Processor.
But if there are "too long" (300+ KB) chapters in your source document, Atlantis might save each of them as multiple XHTMLs.
The check for "too long" chapters can be disabled in Atlantis. Here is how to proceed:
1. Close all running copies of Atlantis (if any).
2. Press WinKey+R to open the "Run" dialog.
3. Type "regedit" (without quotes), and press Enter.
4. Open the following registry key:
HKEY_CURRENT_USER\Software\Atlantis Word Processor\LoadSave
5. Double-click the "Ebook300KB" value, type "0" in the "Value" box, and click OK.
After that Atlantis would not check your documents for "too long" chapters when saving as EPUB. But note that older eReaders might have difficulties with opening EPUBs containing 300+ KB XHTMLs.