I don't understand why you believe a contradiction exists. If the thing created good has been acted upon by another agent and that act takes away from the originally intended goodness, that act would be termed evil. Now if you are refering to a designed process and not an object, then you would have to know if the intent of that designed process made room for fluctuations in the process. For example the weather and changeing seasons. Individually taken, the four seasons are in conflict with one another. However, considered as a whole process they are quite complimentary.
This idea of harm being the determining factor in deciding if evil has occured is flawed. Harm, pain, and suffering can occur without direct evil involvement. Take fire for example. Is fire good or evil? If someone is burned in a fire does that make fire evil ? Of coarse not.
I must reiterate, you must maintain the distinction between moral and metaphysical. You can't combine them when you are trying to define good and evil because they are 2 comletely different perspectives.
The only thing that determines good and evil is intention.
Very simply, if there is no suffering then there can be no evil. The problem of evil doesnt concern misguided or errant intentions, it identifies the existence of suffering and the lack of compassion in the presence of an all loving and benevolent God. That is the contradiction.
The only thing that defines evil is suffering: no suffering, then no evil. And the only thing that defines good in the context of evil is a lack of suffering.