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The only way sewage can back up into a toilet if from the septic system. This usually happens when there is a stoppage and a little used system is more likely to clog up
A toilet won't back up if it doesn't have any water in it. At least no water can't cause a back up. No water in the bowl can allow sewer odor into the house that's all. Your situation is unusual and if you're sure there nothing else hooked up the the septic then the only other way for water to get into the tank so it causes the toilet to back up is from ground water infiltrating the tank or backing up into the tank from the leaching field.
Won't hurt to try flushing the toilet. What you can do to prevent an overflow is remove the cover to the toilet tank and push the flapper down to stop the water from going into the tank if it looks like it's going to overflow
Like I said in my last reply ground water could be a cause of the back up. But if you don't have town/city sewer then I'm skeptical that this is the only bathroom on the septic