Replace is a tool that can nondestructively convert materials from one type to another. It cannot draw on empty space.
Using the Replace tool with Delete, you can safely remove particles from Rigid without causing it to collapse.
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The Replace tool seems to only change the Material code and/or Color for a given particle, leaving the rest of a particle's values unchanged (unless Rigid is involved). Properties such as velocity and spin will be left unchanged. See File Manipulation for more details.