I don't know, it's something that I never do.
When you say you've got 54000 rather than 27000 tracks are you talking about syncing with winamp? If not, the following is of no use to you.
I once had this, because it was scanning a folder with all my music in and then decided to scan the sub-folders, I never worked out why.
You can check this by going to Library>media library preferences>local media>Watch folders and checking which folders it's scanning and deleting any duplicates, then library>delete missing files.
Hope that helps.