If you use automatic syncing, the shuffle syncs based on how you set up the "tabs" for Music, Podcasts, etc. These tabs are in a row near the top of the iTunes window, when you select the shuffle in iTunes. For Music, can you set up syncing based on playlists, artists, albums, and genres. A simple way to do it is to create one or more playlists (in iTunes) with only the songs you want on the shuffle. Select only those playlists on the Music tab, and Apply the change. Your shuffle is synced to contain the songs on those playlists. When you want to add or delete songs on the shuffle, simply update those playlists and then sync the shuffle.
If you use the manual method (by dragging songs and other items to the shuffle in iTunes), you have to also delete items manually. Select the shuffle in iTunes so that you can see its contents listed below the shuffle (in the sidebar), by category. To delete songs, select Music under the shuffle. Over to the right, select the song or songs you want to delete on the song listing. Hit the Delete key.
NOTE: That's for the current 4th gen shuffle (and 3rd gen). It is a bit different for older shuffles, so please post back if your shuffle is 1st or 2nd gen.
I was unable to see myiIPOD when I plugged it in and started itunes. There are many posts that seemed similar to mine but not exactly. I found that all my issues were related to not knowing how to use / navigate itunes. These are the steps I followed.
Deleted and reloaded itunes
Clicked small almost invisible icon in upper left corner and clicked "show menu bar"
Clicked "view" on the menu bar
Clicked "show sidebar"
Clicked iPOD icon
This took me to the settings page. Ididn't realize that the words "On This iPOD" was a button. I thought it was a sentence " Settings on this iPOD " DUH. Oh well live and learn. Then I could see all the songs on my iPOD.
Clicked "On This iPOD" Which is in the top navigation bar next to "Settings"
After all this I was able to:
See my iPOD
See the songs on my iPOD
Add / delete songs from my iPOD
Plug you iPod into your computer using the USB cable. Go onto iTunes, you should see something like iPod shuffle or name's iPod or whatever you've named it.
Click on music (it should be just underneath where it says your iPod) this should show you all the songs you have on your iPod. Click on a song that you want to delete off your iPod and press backspace or delete on your keyboard. A note might come up saying something like do you want to delete songs from your iPod shuffle, press yes.
Hope it helps.