We never saw Charlie do anything on that scale. Changing people is one thing. Changing something of the PK's size made of neutronium is something else.
We did not need to, since his episode had him manipulating or removing things no matter the scale, from Phasers to adult human beings. That, and his destruction of the Antares made him a teen only limited by imagination. What would stop him from making large parts of the DM's hull vanish--which would expose its internal mechanism, probably destroying it in the process? The DM is just a device--a weapon, but Charlie has human thought on his side, giving him near endless advantages backed up by his gifted abilities.