It sounds like Briss doesn't actually split the image files in the PDF (it it seems like just marks parts of them as separate pages, which is why the return to double pages when you convert to ePub). If you still have the original scans and don't mind remaking the PDF, I use
Scan Tailor to process all of my scanned book images, it splits the images, straightens them, crops them to just the text, adds margins, and cleans them up.