The problem with pausing the clock when disconnecting the connection with the user is that the user can simply disconnect his computer from the Internet each time he receives a new question, and then reconnect as soon as they work out an answer.
One thing you could do is give the user a certain amount of time for each question.
The clock starts when the user successfully transmits the question to his browser, and if the user sends the answer before the deadline, he is accepted, otherwise he is invalid.
This would mean that if the user lost the connection, it would only affect the question that they are currently using. But it also means that the user will not have flexibility in how much time they want to distribute for each issue, you decide for them.
I thought that you could do something like removing a question from the screen if the connection to the server was not already alive, but the user could always simply remove the screen from the question before disconnecting.
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