To remove all current influences on a specific layer of the map, you can call Sandbox.ClearInfluenceMap. Influences on the map will not decay with time; so typically, you must clear the influence map before calculating a new spread of influences:

Sandbox.ClearInfluenceMap(sandbox, influenceMapLayer);

Visualizing what occurs when clearing the influence map; any cells set to any value other than zero will be set back to zero.

A cleared influence map