Most of us know that messing with the substrate in the tank can lead to trouble. While I have never read an obviously correct explanation for this, it probably has to do with a release of microorganisms in the tank.
Old, dirty and compacted substrate can lead to trouble as well, so I take out part of the substrate (let's say 20-30%), rinse and partially add new substrate and back in the tank again. Every part of my tank will be refreshed every 12-18 months or so to try and avoid any 'old tank syndrome'.
My hobby hack is that I purchased a 2 meter long 16/22 mm hose, that I use to suck out substrate. As not only the substrate will be sucked up, but also all dirt and organisms go with it, I can keep the rest of the tank and water column as clean as possible in the process. This as compared to scooping up substrate, that will give a lot of pollution released in the water column and I imagine unnecessary risk of algae blooms, diatoms and the like.
Of course, after rinsed and partially renewed substrate back in the tank I will do one or two big water changes.