It is better to modify the contract to add the equipment. Or would the contractor need to hold onto the equipment until a new contract can be awarded to repair the equipment sent in error?
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You have two possible options since you said this is sole source and out of scope. You could use FAR 6.302-1 Only one responsible source and no other supplies or services will satisfy agency needs and get a Justification and Approval (J&A) approved and use a bilateral modification to add the repair to the contract. The second option is a second contract for the repair work, but if it is sole source it will still be awarded to the same contractor. I think the quickest route would be a modification.