Yes, just copy the song on the library (long press, select "Copy Song" at the top of the screen), then adjust the page order for each instance of the song to only use the pages you need. That should preserve annotations for the pages you keep. If you need to ensure each song is using a unique PDF, there is an option in the rearrange pages screen (tap the three dots at the top right) to save the changes as a new PDF.
Mike
Mike