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You should be vacuuming your gravel with each PWC, at least to some degree in my opinion. All the food and waste that settles in the gravel needs to get out of there somehow.
The good bacteria stick pretty well to the gravel surface. You might remove a small portion with a really vigorous gravel cleaning, but not enough to to do any damage. There are lots of other things to look at if you are losing fish. How long has your tank been set up? Test results for pH, ammonia, etc? How big is the tank?