This situation usually occurs when you open a project from one computer to another. If the MIDI configurations aren't identical on both machines, Cubase will present this window so that you can route the old MIDI destinations to one (or more) on your current computer. However, it can also happen with templates that are saved with one configuration, but are then opened when Cubase has been assigned a new configuration.
The easiest way to solve it is to change the missing port to a new mapped port, and make sure to click the Map Always option.
I hope that helps.
MattLTH