If we are placing instances with Geometry Nodes, applying this modifier will destroy all the instances.
Geometry Nodes tree with instances before applying the modifier:
If we apply the Geometry Nodes modifier now, all the instances will disappear.
To fix the instances and turn them into real geometry, we need to put a “Realize Instances” node before the “Group Output” node.
Now the Geometry Nodes modifier can be applied without losing instances.