If you make instanced copies of a bunch of objects (alt+D), then it is possible to give them different Object Indices from their originals. This is useful if you are using Object Index as a mix factor in the material of the objects. This is especially useful when working with multiple Scenes. However, Instanced Objects don't copy all changes from their originals. If you make a change to a modifier, or Transform the original object, it does not update the Instances. So as you are working, you are stuck constantly re-creating the instances.
You can get around this problem by instead using a Collection Instance of all the objects you need copied. Then any changes are reflected. But then you can no longer change the Object Index of the copies. You can set an Index on the Collection Instance itself, but this doesn't effect the objects within it.
Is it possible to somehow get at the Objects within a Collection Instance and give them their own Object Index that is different from the original object?