New Windows install and now I have multiple copies of songs on my iPhone

Can anyone help me out? My solid state hard drive died a few weeks ago and I finally got a replacement yesterday. I installed iTunes and was lucky to have my old iTunes library.xml file backed up, which let me quickly get back up and running with all my music and metadata like play count. However, when attempting to sync my iPhone, it seems like the music that had been on it after the last pre-crash sync is considered part of a different library? Not only did none of the play count numbers for those songs update in iTunes for the weeks I had been listening to the same few songs over an over, but now I have two copies of all of them on the phone. These duplicates do not show up in iTunes. Is there any way to consolidate these songs? Thanks!

The cause was probably a USB glitch during a sync or when copying. The music resides on the phone in separate files. A master file contains a database with an index to the music, an entry for each track and a "pointer" to the file containing the track. Somehow the index got corrupted with duplicate entries. It's likely that the music itself wasn't duplicated, but some tracks had more than one entry in the database. I've seen this happen when syncing (rather than manually managing) also. In my case deleting the track from the Music tab in iTunes, syncing, then adding it back fixed it.
A related problem I've seen is an album may be split, with some tracks in each of 2 or more album entries in the listing. Fixed the same way.

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