Sounds like a good thought but with using some care. You are correct that a tank is much easier to upset when semi-new.
So , maybe some things to help. Can you see through the canister if you shine a bright light on the sides. This may show how much debris is collected and give you a headsup on how bad cleaning is needed, maybe not.
But if it seems right, I would go this way. Do not do it at the same time as other work. Rock the boat but gently?
Be sure to not "work" the soft items too hard and certainly use water without chlorine, not tap water. Get the heavy stuff that will block flow but maybe leave some of the stuff that you would rinse out thoroughly at a later cleaning.
Most likely you will lose a bit of the bacteria but most of us are not running super close to the edge and the small hit it takes will grow back very quickly so that no hint of trouble would be expected.
But on first timer things, it is always a good idea to watch the fish afterward, just to be paranoid! If they begin to show signs of any unusual action, a water change to remove/reduce any ammonia spikes will get it cleared.
Congrats on being aware and asking first as it is lots easier than after one has a group of sickies!