You didn't mention what size tank, what kind of filtration, planted or not, what kind of fish, and what are the fish eating?
If the tank is not planted, vacuum all the gravel thoroughly. Change 50% of the water once every week adding conditioner to the new water. Note that in really huge tanks you can't remove the entire 50% at one time, so the tank size is important.
Beneficial (nitrifying) bacteria live almost exclusively in the filter, very little in the gravel, and not to any appreciable degree in the water column. Gravel vac and water change will not "undo" your cycle. Detrius and decaying food in the gravel are not good for the fish, neither are the nitrates that are building up in the water unless you have lots of live plants.