jjdubs
Here's my  TTSSEQ.ini file contents after Sonar re-creates it and the system is working:
 
[MIDI Input Devices]
0=nanoPAD 1 PAD
1=Oxygen 49
2=Oxygen 8 v2 MIDI In
3=Oxygen 49 MIDI In
MaxInPort=3
[MIDI Output Devices]
MaxOutPort=-1
[MIDI Echo Devices]
MaxEchoPort=-1

If your start Sonar with this file already in place, which keyboard are you missing, "Oxygen 49 MIDI In" or "Oxygen"?
 
You can try to edit the file, replacing "not detectable" device. F. e. "Oxygen 49" -> "Nxygen 49". Or remove it completely. If Sonar is able to redetect it, after locking the file you will be forced to re-enable only one keyboard or Sonar restart (instead of all). Not perfect, but less work...
Other options to try: enable "User friendly names" and/or change the order. With some luck Sonar can start to work without file reset...

Welp! Apparently the problem was Sonar Pro didn't take kindly to projects that were originally created with Sonar X3. Somehow that had never occurred to me.
 
So all seems to be well, now, at least for the time being. 
 
Thanks everyone for your help!
 
John

OK, maybe not. I quit. :-/

Well, it seems the latest update fixed the problem. Actually I did two updates, one Windows and one Sonar. So ...