ITunes sync losing my songs?

After having some issues (question/info here), I decided to continue trying and synced my iPod 2 more times. It finally finished syncing my songs, but there are still 3 missing that as far as I know, don't even show up..
Windows Explorer tells me there are supposed to be 4543 songs. (Full Collection)
When I drag them onto iTunes, iTunes states there are 4542 songs. (1 Missing, Unknown)
When I sync my music collection to my iPod, the Music app says there are 4540 songs. (3 Missing, Unknown)
Where are my songs going? Is there any way I can find out which songs aren't moving over, and any way I can get them to do so?

"If I sync my iPhone with iTunes, will my songs be deleted from my iPhone?"
Yes, everything will be deleted from the iphone.
It has always been very basic to always maintain a backup copy of your computer.  Use your backup copy to put everything back.
If for some reason you have failed to maintain a backup copy, then you can transfer itunes purchases from your iphone to your computer.  File>Devices>Transfer Purchases

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    how do I move songs from Itunes to Nano without losing my songs?

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