I know this can be done programmatically (not sure if this would cause issue or not). Does anyone know how to manually add and configure the COM port index and module position under the SerialPortService?
This is a good question and I am not sure I know the answer but I believe you do not want to make changes here. Configurations you make in driver/network components that need to access the COM ports are negotiated (if that’s the right word) behind the scenes and the result is seen here. Do note the actions on the parent SerialPortService node. If you think what you are seeing is not accurate or not up to date, you might be able to afftect this through those actions.
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Cheers @Eddie, the issue we were having was that the JACE was not picking up the additional COM module. So we wanted to try and manually set the port reference to see if this was a JACE issue or an issue with the COM module.
In the end, we clean dist the JACE and re-commissioned it, and it picked up the COM module. It was a strange one! We did try the actions; however, we didn’t have any success 
. It’s a mystery left to the DDC gods.
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which version of daemon?
I was using 4.7 when I had this issue.
Did you use the same version of workbench to access the Jace? Maybe upgrade to 4.10u.x long term support
Unfortunately they didn’t want to upgrade. In the end we recommissioned and it recognised the extra module. It was a weird one… probably a bug somewhere.