Yes, simply store the time at which your app was closed and the time left to count down in NSUserDefaults. When the app starts again you get the time it was closed from NSUserDefaults and the time left. Using the current time it's simple math calculating the corrected time left on your count down.
Something like this might do the trick, untested of course:
// save state
NSUserDefaults *userDefaults = [NSUserDefaults standardUserDefaults];
NSDate *now = [NSDate date];
double countDown = 45.0; // in seconds, get this from your counter
[userDefaults setObject:now forKey:@"timeAtQuit"];
[userDefaults setDouble:countDown forKey:@"countDown"];
[userDefaults synchronize];
// restore state
NSUserDefaults *userDefaults = [NSUserDefaults standardUserDefaults];
NSDate *timeAtQuit = [userDefaults objectForKey:@"timeAtQuit"];
double timeSinceQuit = [timeAtQuit timeIntervalSinceNow];
double countDown = timeSinceQuit + [userDefaults doubleForKey:@"countDown"];