Trees too deep in the ground, an all too common problem, have two basic problems. When the trunk flare is under ground, it stays moist and doesn't breathe properly as bark is supposed to do. Soil too high on the trunk also often hides circling and girdling roots which choke the tree and drastically slow down growth. Many trees are snapping off at the ground surface because of this problem. Trees grown in containers are highly subject to this damaging condition. To make matters worse, mulch is often piled up on trunks.
Soil too high on the trunk also often hides circling and girdling roots which choke the tree and drastically slow down growth.
Solution? Get the mulch and soil off the trunk and off the flare. If you do the soil removal yourself, use hand tools and gloved hands being extremely careful not to damage the wet bark tissue. Water can be used but only with a soft flowing stream. Strong water blasts can severely damage the soft bark on the base of the trees. The best route is to hire an arborist that uses the Air Spade. It is a fancy sandblasting type tool that blows air (no sand) at a high velocity and removes the soil without damaging even the smallest roots. Arborists that don’t use this tool or the Air Knife should be passed on when hiring a tree care company.
Once exposed, the root flare area should be left exposed to the air. The tree trunk and root flare eventually will grow and expand to fill the depression around the base of the tree. Putting anything into the depression will cause the area to become a problem again. That includes stones, bark, compost or anything else. All I would put in the depression is a very thin layer of shredded mulch and that can be skipped. Deep holes that may create a dangerous situation need to be covered with a grate.