Comment it. Javadoc it. Name the method appropriately so that it suggests that the parameter will be changed.
For instance: Collections.sort(myList) in the standard Java API does exactly that.
If you do modify your treatment return the result list from the method, then make sure that the list passed in is not changed as a side effect.
If I see: List myMethod(List inputList) I would assume that my inputList is unchanged, and the return value has the result after copying the inputList and modifying it.
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