I also had this, like described in this thread.
Still I wasnt able to find out what happened and what caused it. I used the update button on the webapp and in my case it got stuck uploading to arduino and didnt change until I tried the fix with a new upload via USB.
After a few tries it worked out and I was able to upload sketches to arduino again. This issue still didnt appear anymore so its hard to find out more 
What I did to fix the problem:
-Connect Arduino to the PC, make sure that the right Serial Port and the right Arduino Board is configured.
-Open up a new sketch
-Click upload
Now it should compile for a second as you can see in the logbar.
When you can see that it starts the upload, instantly click the Reset button on the Arduino.
If you were too late, the upload seems to get stuck and probably gets timed out. Unplugging the USB cable will instantly abort the process.
Just try a few times, its not easy to find the right moment.
Maybe there are better ways to fix this, but since I only had this once I didn’t search any further.