We modified the ConfigurationSetup.cfg file to point to a networked workspace as a Custom Configuration. Then, we had to reinstall the refresh and apparently that process clobbered our customizations.
So, what is the recommended approach to customise a configuration so that an update to the software will not remove our customizations?
I install our installations and even updates by using a batch file to initiate the install. We too have a "pointer" file for networked resources. Knowing that in the past Bentley overwrote delivered files I have a copy of our needed configurations on the serve to copy over after installation or upgrade. I also run other things from within the batch file. but most of it is personal preference.
I do not run the update from the CONNECTION Client as I have the options to show updates turned off for each user. I instead create the install with the / layout switch so I do not have to download the components each time. I then run this from a location on the server.
By using a batch file for me ensures that I have the best chance to install our cad products the same each time and therefore to hope make support easier, or same, from machine to machine.
All this to say, once you have a working cfg copy it out so you can place it back at anytime needed no matter how you choose to get it there.