If I unplug a USB keyboard, I can't just plug it back it: it won't work unless I completely reboot my PC (and Sonar).  (I don't do this on purpose—sometimes the plug just pulls out.)
 
What's worse, if I even change a USB drive in another port, it makes my USB keyboard stop working and I have to reboot my PC (and Sonar).
 
Why is this and is there a fix?  This is extremely annoying as it takes a long time to reboot the PC, restart Sonar, and reload the project.

Do you have USB power management turned off?

Sounds like a PC problem not a Cakewalk problem.
 
Try and see if another PC keeps the Keyboard alive when unplugging and re-plugging.

Two possible fixes:
1) PS2 keyboard (usb to ps/2 adapter)
2) enable Legacy USB support in bios

Edit- Just clued in you are talking about a usb midi device not a qwerty keyboard. ( duh). In which case I would change 1, above to use a conventional midi interface. I have the same issue with my usb musical keyboards, but I can disconnect and reconnect my midi interface devices with no problem. In one case I power the device with usb to avoid another wall wart but communicate via 5 pin midi.

One for the hardware forums....

I don't see this as primarily a hardware issue Alex. Windows seems to govern USB ports in a certain way which in turn affects how SONAR behaves when a USB device is unplugged. As I noted above, MIDI (5 pin DIN) devices don't seem to be affected and can be plugged in or disconnected/reconnected without this issue - at least those I have used here. FWIW this is into my Audiobox 1818 VSL MIDI ports, and into my Cakewalk UM -3G's (both of which, curiously, are USB devices themselves - which leads me to think that maybe Cakewalk could improve something in the way Cakewalk checks/rechecks for USB devices if one doesn't immediately show up in a project.)

A pleasant side effect of using a wireless keyboard/mouse is that turning them off/on doesn't bother anything running.  I'm sure this is because the bluetooth doodad stays plugged into its USB port and keeps that subsystem happy. 
 
It's also cool that one less USB port is being used by the pair.
 
The only downside I've experienced is flaky behavior when the batteries run low.  Checking and keeping fresh batteries in them makes it all quite painless.  For me anyway.
 
 

Could be you need to clean out old USB device files...
 
http://www.thewindowsclub.com/usboblivion-remove-usb-traces-windows
 
http://www.techspot.com/community/topics/usb-drive-or-flash-problems-how-to-cleanup-and-remove-old-usb-storage-drivers.145884/
 

Brando
I don't see this as primarily a hardware issue Alex. Windows seems to govern USB ports in a certain way which in turn affects how SONAR behaves when a USB device is unplugged. As I noted above, MIDI (5 pin DIN) devices don't seem to be affected and can be plugged in or disconnected/reconnected without this issue - at least those I have used here. FWIW this is into my Audiobox 1818 VSL MIDI ports, and into my Cakewalk UM -3G's (both of which, curiously, are USB devices themselves - which leads me to think that maybe Cakewalk could improve something in the way Cakewalk checks/rechecks for USB devices if one doesn't immediately show up in a project.)

Regardless sorry not a Sonar issue. Sonar does not stop keyboards from working :)
Window HAL and related drivers is responsible, or the hardware itself (= hardware forums).
The giveaway is where the OP states "it won't work unless I completely reboot my PC", it's HAL.
 
USB with midi/audio devices are a completely separate matter.
 

Ta.

Thanks for all the thoughts.