When overwriting fixed-sized values like integers or floats, the old value can simply be overwritten. Holes are only left if the overriding values do not fit in the old location (strings, byte arrays).

To clean up unused space, you start an iterator at the root of the document and recursively write to a new buffer. This will clean up all the unused space. This operation can be delayed by the application for as long as they wish, until the size trade-off outweighs the cost of rebuilding.