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Rack Optimization, as the name suggests, consolidates all the data for discrete inputs and outputs in one chassis into a single I/O connection.
You can still add individual Module connections for analog modules or specialty modules or even discrete modules with their own standalone configuration requirements. You don't need to delete or modify that Rack Optimized connection.
Yes, adding those Module connections does generally require the ControlNet to be re-scheduled (a download to the CPU and a re-schedule calculation and save by RSNetworx for ControlNet) if you want them to be scheduled connections.
Rack Optimization does make a substantial difference in efficiency, if not performance. If you had a 10-slot chassis with 9 discrete modules, Rack Optimization allows you to control them in one cyclic I/O connection instead of 9 separate ones, each with their own configuration packet and overhead.
It's not as important in modern EtherNet/IP systems except for the CPU load on the network module, but with good old 5 Mb/s ControlNet it made a difference on medium and large networks.