I had the same issue crop up today out of the blue. I changed nothing on my PC or otherwise - I just started getting the error message "flashing is taking longer than expected try pressing master_reset button"
I updated the firmware per ballscrewbob's instructions on the following post: Arduino 101 Uploading code timeout erro - Arduino 101 - Arduino Forum
I also removed and reinstalled the Arduino plugin.
The online editor now works.
In 25 years of working with PCs, I've seen time and again how $#!+ happens for no apparent reasons. Frustrating for sure.
ballscrewbob - thanks for your help here - this is the second problem you've helped me resolve. Appreciate your contributions to the forum.