Within the LocalServerManager config through the RateLinx console (Add-in Config Dropdown), you should be able to set a new appSetting property with an id of "LicenseWSURL" and then the appropriate address for the license web service to use (shiplinx.shipsource.com/LRMT/License.aspx). Also need to add "SLX4ExportClientID" as an appSetting and value "ShipSource"
For ShipLinxSetup and refreshing the license, a config setting will need to be added within the web.config for ShipLinxSetup (C:/inetpub/wwwroot/shiplinxsetup/web.config). The setting name will be "LicenseWSAddress" and will need a value that points to the ShipSource license web service address. (shiplinx.shipsource.com/LRMT/License.aspx)
Refresh License, then try to open ShipLinx again.
This popped up again the next day, and the only thing I ended up doing was checking the "Use Remote Licensing" option in the ShipLinx Web Setup->Server Config page.