You have several options. For example cookies can be used to store data between pages (or same page) even when refreshed. You only need to store the start time of the timer. You can calculate the time between from the current time minus the start time. So it will have the correct countdown value, even if a user browses to another site and comes back some time later.
For more info on persisting data in the browser, have a look here:
http://www.sitepoint.com/html5-browser-storage-past-present-future/[
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Good luck!
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