How many ebooks are you talking about (millions)? Is there just a question of finding duplicated files? That’s easy with a shell script. For metadata, see if the books already have it since a lot do. After that, you can use fairly crude hacks as an initial pass at matching library records. There’s code like that around already, try some web searches, maybe code4lib (library related programming) if that is still around. I saw your earlier comment before you deleted it and it was perfectly fine.