I had the exact same issue. The device manager showed the comports, but it did not appear in the arduino IDE.
My situation was that I tried to read some data through Processing from an Arduino Uno and an Arduino Pro Mini. I was using a USB hub to read the data from both devices. There were couple of times the processing ran into Null Pointer Exceptions and some other errors while reading the data. After that I started getting the issue. Also sometimes the both devices didn't detect well when I used the hub.
Solutions : I disabled the comport for the Uno on the Device Manager. Then enabled it again and it worked ok. Also, using a hub did not work robustly for the two Arduino's. I used two different USB ports on my laptop and it worked well (but it worked well with one Arduino and other devices like mouse and keyboard on the USB hub)
Sometimes you get this error when you try to read the Serial Data from another program (like Processing in my case) and crashes. I think this is because the Serial Port is not released by that program when the error occurs. So try everything possible to make sure the port is released to run it again.
Hope this helps