Several users have reported, and we have experienced in-house, an issue where iTunes fails to transfer all selected tracks to the iPhone, though the application indicates that it has done so. In these cases, the user will be left with a subset of music synced to their iPhones.
In some cases, the fix is as simple as re-creating the iTunes Library, as discussed in Apple Knowledge Base article #93313.
In other cases, you may need to actually delete then re-import the Library, via these steps:
- Quit iTunes
- Backup your iTunes library (~/Music/iTunes under Mac OS X, \Documents and Settings\username\My Documents\My Music\ under Windows XP and 2000 and \Users\username\Music\ under Windows Vista) to a separate location (can be on the same volume)
- Launch iTunes while holding down the option key under Mac OS X, or the Shift key under Windows and follow the steps to create a new library
- In iTunes, choose Import from the File menu
- Select the backed up iTunes music folder as a source folder
- Restore any deleted preferences