My library is in four actual libraries - Adult Fiction, Adult Non Fiction, SciFi and Children and is about 35K books. It was given to me and previously maintained under Linux or Unix hence the huge number of extra long filenames (which Windows does NOT like). Like over a thousand books are "lost" accordingly. I can't see anyway to rescue these books except manually
There is SOME duplication in Adult Fiction and SciFi and the formats are generally in pdf, txt, mobi and epub formats.
The Adult Non Fiction library is about 10K books and 70gigs. I am cleaning them up but haven't tackled this section yet.
I intend to merge them all into one library in the not too distant future (unless someone convinces me otherwise

). I have already merged Adult Fiction and SciFi.