If the runway is contaminated, snow/slush then flaps should be left out so that we can see if there is any accumulation of snow etc on or around the flaps. Plus if you retract them and they are full of this stuff and it subsequently freezes there could be problems.
I would have thought that you catch the possible contamination on the taxi in and shutdown. Then they'd be retracted and shouldn't be extended again until the B T/O check.