I would like to connect a probe of an ILA instance in native mode to individual nets of a net/bus bundle.
To do this I expand the interface on one of the connected modules and then add a net between the ILA probe and the desired pin of the interface.
However, now the original connection for that pin seems to be disconnected.
This is expected behavior.
Whenever you connect a net to any of the expanded pins of an interface it overrides the interface.
When validating the design you should see warnings similar to the following:
To use the ILA probe on a single net of the interface, make the override net connection between the correct pins of both expanded interfaces and then connect the ILA probe to that net.
For additional information see Chapter 6 (Using the ILA to Debug IP Integrator Designs) of (UG994).