iTunes will not copy from an iPod to the iTunes library.
Did iTunes delete the music from the iPod?
That would be the expected behaviour if you told iTunes to automatically manage the music on that iPod when it asked after it was first connected to your computer.
What that does is to make the iPod look like your iTunes library, so new music in your library gets automatically copied over, and music you've deleted from your library gets deleted form the iPod.
So think what happened here. You connected the iPod, iTunes saw all that music on there and had been told to automatically manage the iPod. So it thinks that that music is stuff that you've deleted from your iTunes libary and so it then deletes it from the iPod to keep your library and your iPod looking the same.
If you want content on your iPod that you don't have in iTunes then you need to manually manage the music on it. Follow the instructions here:
support.apple.com/kb/ht1535
If you want to get music off of your iPod and onto your iTunes then you need to be a bit clever, not particularly clever but it's not a a completely simple process.
The exception to this is that music you've bought on your iPhone should transfer to iTunes when you connected the phone to the computer.
Mine didn't do that with the last thing I bought though, but that said it didn't delete them either.
So how did that music get onto that iPhone?
Did you buy it on the iPhone?
Or did you buy it on another computer and then connect the iPhone to a different one which then blanked the music?