There are three ways to create boolean operations between two elements:
If the source geometry consists of several closed parts and one of them has disappeared, click the button with the cursor icon in the Source section and select the part to which the operation should be applied.
To create an operation at the object level, first select the cutter (the object that will be connected to the second input of the node), then the source object, and run the tool.
To create an operation in the SOP container between two nodes, first select the cutter node, then the node with the source geometry, and run the tool.
If only one node is active in the SOP container, but there is another node with the Template flag enabled, it will be used as the source geometry.