To reset the clock, I've been using the 'Set Time' sketch in the examples of the DS1307 RTC library.
I pull the controller, load & run the sketch, reload the light controller sketch and put the controller back in service.
Probably unnecessary...probably misunderstanding something...but it gets the controller back closer to actual time.
I don't recall ever seeing the RTC not running message. It's possible I never checked for that.
I just now pulled the controller to clean up some temporary wiring and I added the setSyncinterval command as we discussed earlier. I'll see how it runs for the next week or so.