You typically have bacteria in your filter, gravel, and water column. So it would just depend on how much cleaning you did. While cleaning out a sponge in a bucket of the same tank water won't get rid of all of your bacteria on the sponge, you might lose some just by getting some of the gunk out of the filter. That being said, unless your tank is seriously overloaded with fish or you don't have that much filtration, and you did a major cleaning, it shouldn't have an impact.
Regardless, it never hurts to have a bottle of a live bacteria culture handy in the event you have something nasty hit your tank and you decide to nuke it and start over (completely drain and clean the tank, gravel, filters, etc.)
