If it's only day 3, I don't think any damage was done. Eggs are pretty hardy and can hatch under a variety of conditions. I'd just regulate the temp from here on out, you should have the desired temp at this point.
I wouldn't run the temp higher than normal to counterbalance, I'd just keep it at the desired temp. I've had broody hens be off the eggs quite a while and still have good hatches. How low was the temp, and what day are the eggs on?