Lock midi ports

I get the problem. Indeed, Sonar does not associate device names to port numbers. In a recent update there was an attempt to address this but I don't know how successful it was.
 
In the scecenario you are describing you would like Sonar to know that the Deep mind USB is the same as the Deep mind connected to the USB port of the A-Pro. That can't happen. They are entirely different inputs and outputs.
 
The ttseq.in is where the midi I/O assignments are stored. You need to re-order your midi inputs and outputs so that they are where you need them, then backup the ttseq.in for that setup. Midi outputs are easily re-ordered in Sonars preferences. The only way to re-order midi inputs is to edit the ttseq.in using notepad.
 
Firstly, the simplest solution would be to have the devices connected how you will use them, set the port order how you want them, exit Sonar then backup your ttseq.in file.
 
If you do wish to be able to change them easily, first plug everything in as you normally use it with the midi I/O where you need it then exit Sonar and make a copy of the ttseq.ini.  Next plug in the alternative setup using the Deep mind USB. Make sure the midi outputs are in order under preferences, then exit Sonar. Now make another backup of your ttseq.in.  Open both of the backup copies of ttseq in notepad. Comparing the two, find the midi input port order settings. Re-order the second version with the addition of the Deepmind USB how you need it (so that the Deepmind usb now takes the port number of the a-pro usb where it was previously located) Save the edited file. Now you have two backup copies of the ttseq.in.  Put one in a folder lebelled something like 'Deepmind midi' and the other 'Deep mind USB', along with a shortcut to the ttseq.in folder location in Sonar. Now, when you want to use Deepmind USB, before you open Sonar go to the 'deepmind USB' folder, right click on the edited ttseq.in file and choose "copy", click on the shortcut and paste it over the ttseq.in  Sonar. That's it.  When you start Sonar your ports will be in the correct order. Use the same method to switch back to your other setup without Deepmind usb.
 
It is a bit of a hassle to get your head around, but it is quick to load and does work perfectly once setup. I use it to change large amounts of midi I/O whilst preserving port order for remotes etc. Whether it is worth it to change a connection method just on a whimsy with no real advantage is up to you:)
 
Hope this helps:)
 
 

Did you try making TTSEQ.ini read-only?