I have only used BioSpira here so ymmv, but they say to shut off a skimmer in particular for 48 hours. My argument here is that the cycles can take upwards of 1 month to complete. Using the skimmer for 28/29 days I would hope doesn't deplete their bacteria, especially if they allow the water and foam to circulate back into the tank as it breaks in. Bacteria will reproduce in various other areas of the tank such as the sand, the rock, and on other hard surfaces. The bacteria in the water column would be small in comparison.