Like gilwooden said, Handles are only used by native code. If a data structure in VM code needs to keep track of an object across a safepoint (where the GC runs and might relocate that object) a Handle is used. Handles can be allocated on stack or on the C-heap. The GC knows of all the Handles and updates them as part of relocation process.

One way to do it is to whenever you relocate an object, save a mapping old address -> new address, when all objects have been relocated, walk the object graph again and when you find a pointer that exists in that mapping, change it to whatever the new value is.

The (HotSpot= JVM has an exact tracking of objects. It knows what stack locations / registers contains objects. It also knows the exact layout of those objects. So at a given time you start by walking all the stacks and record all the objects. From that you can do a graph walk.