Synchronizing multiple music libraries can be tricky if your music is not well tagged or has come from many different places. Files may be missing identifying tags, some tags may be out of synch, or named slightly differently, or the same album may be encoded different ways. Managing a large library may take several iterations of pruning, copying, checking, and re-importing.
As a general rule, synchronize a few tracks initially and make sure they transfer to the right location. Click "Show All" to force an update... and check that they show up in iTunes, if you're using iTunes.