how do I get the 7890B GC to recognize a new flow controller that I just installed?

From the keyboard, remove the EPC module, reboot, then configure the replacement EPC module. 

When replacing an EPC module or a detector signal board, you will have to update the configuration of the GC. This is because the configuration information includes the unique ID# and 
manufacturing date for these parts.

To configure the new GC module
1 Replace the module (the physical part) and power on the GC. The GC will list the Exceptions to the configuration and indicate that these modules are broken or missing.
2 Unlock the “Configuration locks”.   Options, Keyboard and Display, turn off the configuration lock
3 Press [Config] and select the GC module that you replaced.
4 Press [Mode/Type]. The GC displays Remove module. Press [Enter].
5 A Caution message tells you to reboot the GC.   Unlock the “Configuration locks”.   Options, Keyboard and Display, turn off the configuration lock
6 Press [Mode/Type]. The GC displays Install module. Press [Enter].
7 A Caution message tells you to reboot the GC.
8 Press [Options]. Scroll to Communications and press [Enter].
9 Scroll to Reboot the GC. Press [Yes/On] twice.
10 Navigate to the configuration table for the GC module.
11 Verify that the configuration is correct. Modify any additional configuration items, such as, Gas type or Lit offset.