Yeah your images, videos and manuals should all be fine just don't run the clean up images function from the tools menu until you re-import the games. I think the notes section is directly in the XML (not 100% sure of this) but if that is the case I would guess that the notes are removed with the game entry in the XML but if you haven't edited or made any notes of your own then you would get that all back when you add the games back in anyway.