Be careful...You will really have the chance of shutting the entire place down if anything goes wrong...
Well, you will virtually have to shut the place down anyway, because re-scheduling the network will need the controller in Program Mode.
You can ONLY add Flex I/O into the ControlLogix project OFF-LINE, after which you will need to Download.
Just done exactly this task yesterday, added several Flex I/O rails to an existing ControlNet network.
Here is how we did the task....
Go ONLINE first, then put the controller into program mode, so that nothing can change.
Do a complete Save, including data.
Go OFFLINE, and add the new Flex I/O adapters and I/O modules into the I/O configuration.
Download the project to the controller.
Connect up the new Flex adapters, the I/O modules do need to be installed on their bases.
Start RSNetworx for ControlNet, and "Go Online" to the network. It will poll the network for ControlNet nodes (the "onlink"), then build the "offlink", discovering all the modules.
Carefully check that all the hardware has been discovered by RSNetworx.
If all is present and correct, proceed with re-scheduling of the network.
Hopefully when it is done, the I/O light on the processor should be steady green.