The issue is that SONAR stores I/O port names in the project file based on the way drivers are named and numbered in Windows, and cannot map old ports to new ones automatically. I ran into the same issue when my E-MU 1820m died and I switched to MOTU MIDI and audio interfaces.
Unfortunately, there is no other way of fixing this other than modifying and re-saving each project file with the new I/O assignments.
I'm not sure why the Bakers have never changed this to use 'friendly' I/O names which could be made to match for different interfaces. There must be some significant architectural obstacle.