I charge by the hour for drain cleaning, no flat rate.
I take the time to rod the line back and forth several times through the problem area, and run plenty of water/toilet paper before I call the job done. I want to make sure that I remove all of the clog. I don't spend the extra time to run up the customer's bill, I spend the extra time to make sure I do a complete cleaning job. If everything feels good, everything drains fine, then on a power rodding (not a closet augering) I offer 6 months. Eventually, I will have to come back and reclean a problem line for free that I didn't catch the first time, but a happy and satisfied customer is the cheapest advertisement, IMO.
Now if I can feel problems down there, am pulling back dirt, lots of roots, etc, and the customer doesn't want to investigate further, I would explain the situation to them, and they would get a much shorter warranty. I am not willing to take a soaking because they want to cheap out.