Without knowing all the specifics you could investigate these ideas:
1) Use local storage. When the page loads, have JavaScript check if a certain value or flag is set, etc., and act accordingly. Maybe when the timer begins you set a flag. When it expires, the flag is removed, or value changed.
2) As the timer runs, make an AJAX call (or several) to a PHP script that updates a session variable. When the page loads, check if the variable exists and for its value (maybe some kind of flag).
Hope these ideas help!