There is a patch in the recent eject that should solve this if you own the device (chown `whoami` /dev/devicename).
Anyway, if your device was mounted under /media/usbdisk, do this:
(This just executes "eject /dev/sde" on my system, but it doesn't require you knowing the device name)
After a few seconds your iPod will flash and you'll be ready to go again...
If you already umounted the filesystem, eject will not work. You'll need to try remounting the filesystem and ejecting or just pull the plug and reconnect.