I'd say the run would generally be safe, viruses like hantavirus only last a week in mouse poop, but if the COOP has mouse droppings from the last flock, your best bet is clearing the bedding, and using diluted bleach (only need about 1/4 cup to a gallon to disinfect hantavirus) to clean the floor before putting new bedding down. Make sure no hens are around when cleaning and make sure no puddles are left for them to drink from.
We haven't used our run in 2 years and just started using it again, and there's a vole still living there that poops in abundance! So just because it's been a while since you've had hens doesn't mean the rodents have moved out. Same goes for my coop - abandoned for 2 years, and yet when its dusk tons of mice come raining down from the ceiling! I've set up traps and it's been going good so far. If the pullets are like my last flock, maybe they'll hunt the mice out of the run themselves.
To prevent mice from moving in, try to gather as much food and water as you can before dusk to stop them from getting a free meal. Take note of your hen's feet every morning to ensure they are not being gnawed on by rats. Put feed bags in trash cans and close them securely. That's about all I got.