How do I delete multiple copies of songs on my iPhone when my laptop's iTunes only has one copy of each?

Hi, everyone.
I've seen many versions of this question, but mine has some key differences.
The problem is that my iPhone 4S has multiple copies of almost every song that I've selected to copy from iTunes. The easy answer is to delete all the music from the phone and then re-sync from the iTunes library, except that I don't sync, I manually manage, because I have a 9000 song iTunes library. According to iTunes on my laptop, I have 835 songs on my phone, but there are actually over 2000 on the phone due to the duplicates. The fact that the duplicates do not show up in the iTunes library means I also cannot use the "Show Duplicate Items" tool.
I'm thinking that the only two solutions are:
1. Manually slide and delete all 1200+ dupes on the phone
2. Delete all music from the phone and then go back through the library and cherry pick what I want on the phone. This seems okay, but I don't know why this happened, so I'm afraid it will happen again.
I'd be thankful for any advice!

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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