Hi Rohan,
You're doing things correctly. Solid Element Ops ('booleans') are dynamic, so if an operator is moved, the result is moved. Thus, the only way to see the result of a pure subtraction is by having the cutting element be on a special layer reserved for such things.
When roofs are subtracted from walls with upwards extrusion, for example, the operators (roofs) don't have to be hidden since it is the trimming that is desired. But, with a pure subtraction, you're right: you won't see anything unless you hide the operator. Deleting the operator, deletes the operation as you've seen.
If you make the layer for 'hidden cutting objects' display as wireframe (the wireframe column in the Layer Settings dialog, then you can see the result even as you still see the shape of the cutter and move it about if necessary.
Cheers,
Karl
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