Is it possible to edit an ePub and retain annotations?

I realized too late that there is an error in my ePub file that resulted in MarginNote not being able to change the viewing font for this book. There is nothing wrong with MarginNote I think, although it is a possibility, so I think there must be a tag somewhere in my ePub file that is locking the font into place. Other books render just fine and I’m able to view them in MarginNote’s different font settings.

I was thinking I might take the file over to my ePub editor, Sigil, and change some of the coding tags and see what works. But I’d like to be able to load my many annotations back onto the new file. It would still be the same book word for word, is this a possibility? And if it is possible, how much can I change in a book? Would I be able to fix typos?