Yes, definetely a cleaning is in order when the fry tank gets dirty, but its different than with big fish, and you have to be careful with a few things.
The obvious - don't wonna suck up any fry accidentally with the python. Then there is the water issue - the new water
has to have the same temperature and being dechlorinated than the tank water, and it has to go in really slow. I usually use a piece of airline tubing to get the new water into the tank. Really slow.... so the fry get used to any small differences in pH...