You will need to give some more information.
Did the iPod remove the "Do not disconnect" image, prior to when you disconnected it. You can corrupt your files on the iPod if you don't disconnect properly.
You need to let us know what version of Linux you are using, and I presume that you connect through Amarok. Some versions of Linux will automatically detect the iPod through the HAL demon. Others will have to be mounted.
If things got corrupted on your iPod there is a file under iPod_Control/iTunes which I think is called iTunesDB. If something happens to that, you will have to wipe your iPod clean and reinstall. After your reinstallation you can load your iPod once again.