How do I remedy mold/mildew that has appeared since blocking off ventilation?
The problem is humidity and condensation. Wet air is heavier, sinks, and the basement is cooler, so then condenses. 

You need to dehumidify that air. The easiest solution is likely to buy a dehumidifier and run it constantly in the basement. 

Re-opening the cold-air return can help, as it will circulate some of that moist air out of the basement as well. 

All that said, this could be an issue with ground water as well. Are your walls/floor waterproofed from the outside?