You cannot replace only a single instance of a part in a multi-instanced block. Part replace does a physical swap of the part. In order to do what you require you need to only be replacing properties - in your case this is not possible because the two parts have different part numbers.
You could probably force this by manually changing the part number property and any other associated properties by adding them as instance values when you have the correct instance of the schematic open.
Thanks Robert for the quick answer.
And I can not mark this as a correct answer, then what bothers me is that the user could not be aware that the component is in a hierarchical tree, proceeded with the substitution and have a changed schematic.
At some point the tool has to notice that this substitution is happening in a multi-instanced block. From the user perspective this is not noticable. No indication of multi instance.
What this command does is perfect for flat designs, but dangerous for hierarchical designs. Even Variant Manager is smarter in this regard.
If I send a SR, will this be addressed or just rejected as WAD?
It would be treated as an ER so you would be directed to Ideas - I suggest you post an idea directly. Adding support for instance data in Part Replace is not a simple implementation and was not in the scope of the original requirements.