You can create a special object (for example an invisible sprite), and add NoSave behavior to it. Use this object to run the timer and to store different values in its instance variables, which you don't want to be affected by the saving/loading events.
I have a global variable named TimeRemaining. I set the timer every second as below
When I use a System action called "Save Game", it saves the value of the global variable. This happens when I reach a checkpoint. Now, for example, The game continues thereafter for 10 more seconds before player hits the obstacle. In this case I have to reset the game back to the checkpoint, so I use the system action "Load Game" and mention the slot to load. This leads to resetting all the variables including the "Time Remaining" global variable. I want to avoid resetting this variable.
With your approach it will just save the state of the object but not the variable. Or am I doing something wrong?