The clearance inside the combustion chamber is reduced when the engine block surface or cylinder head surface has been resurfaced. The reduced combustion chamber clearance may allow the valves to come in contact with the head of the piston, resulting in an engine failure. The using of destroked pistons eliminates this possibility. Also in engines where the cylinders have been rebored, the use of destroked pistons eliminates the possibility of the piston striking the head gasket which could possibly overlap the cylinder bore.
The use of destroked pistons with engine rebuilders is very popular, as many times there is no knowledge as to how many times an engine has been rebuilt, or how much material may have been removed from the engine or cylinder head surface.
Many piston manufacturers automatically destroke their oversize pistons, and the use of a destroked piston will not have any adverse effects on the engine performance.
Source: Hastings Piston Rings