Your opponent was inactive for too long, that should not lead to an automatic loss.

[pedro]

I played a game against a strong opponent who was ahead in the end-game and I was only playing untill the end hoping that the flag might be somewhere in an unguarded position. 
At some point the opponent was taking a long time for their move. I guess that they may have lost connection. I decided to wait and surrender just before the end of their time. But while their clock was still ticking and they had more than 2 minutes the game stopped with the message that the opponent was inactive for too long.
I believe that the game should wait untill the full five minutes. And if it is desired that inactivity should end the game, then at least some pop-up window should be shown where a player can choose to decide the outcome (in a similar way that the lichess app does this).

I think having the ability to decide the outcome is definitely a good way to handle these kind of situations.
Lichess and Chess.com are both really nice I use them both daily and they also have tons of features.
The way we handle the inactivity comes from Chess.com. 
As of right now we have the inactivity timer pop up based on the amount of moves. 
We are however still tweaking these values to get them to a point where it fits players on both sides.