I have't run into the "lost icon" thing. The common problem if you disconnect without going through the "Safely Remove" routine is that the computer thinks the device is still there, so it won't connect "another" device to the same port. Since the device you disconnected became "another" (isn't recognized as the same one) it won't reconnect when you plug back in - because the machine still thinks there's something disfunctional on the port.
There is, apparently, some danger of "scrambling" things on the removable drive if you don't follow the procedure. I've heard of it more often with the "flash cards" for cameras, that may "lose their format" if improperly unplugged. I hadn't thought it too common, but have seen some comment about it recently (re. cameras) so apparently it does cause some people some problems.
Often a reboot will clear things, but no guarantees on that. It's possible that rebooting with the drive disconnected, and then plugging in, might clear the port.
The general rule with USB, if things really get fouled up is to disconnect the device, remove (delete) the USB driver/port, and start over. With most USB devices you MUST INSTALL THE DRIVER BEFORE YOU CONNECT THE DEVICE, so that the correct driver is present when PnP detects the device when you plug it in. If you don't have the correct driver already in place, PnP may substitue something inappropriate, and it's hard to "change it's mind" after the fact.
This is all pretty vague, but it may take some searching to see if there's something more specific that you can do.