How did the config file get copied to the system in the first place?
If it was with custom action code then what might work is a repair of the existing installed product. If the CA condition allows it, then the code will be called again and do another copy of the new file.
Otherwise the answer is no. The supported upgrade in a VS-generated MSI is a RemovePreviousVersions major upgrade.
If I knew in advance that updating the config file separate from the product was going to be a requirement, and it's used by an installed application, then I'd make it app's responsibility to have a choice to load a new config file. By tying the config update to an MSI file the design effectively limits the update choices to what's available in VS setup project updates (RemovePreviousVersions).