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The removal of a couple of slave I/O devices will have a negligible effect on performance; there will be a couple milliseconds of reconnection attempt traffic every few seconds. DeviceNet does not pause and retry before moving on to the next configured slave device like some protocols like Modbus do. Ordinary DeviceNet configurations have enough "interscan delay" time between polling cycles to easily accommodate that traffic.
If you want to minimize that effect on a super-tightly tuned network, or you don't want to be annoyed by the error messages on the 1747-SDN for the missing nodes, you could go online with RSNetworx for DeviceNet, upload the Scanlist, un-check the scanlist Active box for the entries for those devices (without deleting the device entries or mapping), then re-download the scanlist.
If you aren't familiar with the software, and don't have archives or descriptions, it's probably best to either hire in an integrator to do that change, or leave the scanner alone.