Problem #1:
Specified MIDI inputs do not save after project shutdown
 
See image below.  I use Notemapper VST (https://www.codefn42.com/notemapper/index.html) as a way to easily combine synth sounds into one part.   As seen below, I have Notemapper simple instrument track on top, which then I have Channel 1 going Bass 1A, and Channel 2 going to Bass 1B (then both to an aux track).  The input echo button needs to be enabled on these synth midi tracks so they can read the MIDI data from Notemapper.
 
Problem is....  Upon restart, it seems like all MIDI track inputs forget their last setting.   For instance, below ALL i have was Notemapper 1 Ch 2 as the input for this track the menu is open for.  But when I restart the application and open the project, it has my MIDI controller input checked!   This causes my bass to play even when I am say trying to play my strings section.  I am constantly having to go in and uncheck these EVERY time as I do not want my MIDI controller to keep controlling these.
 
I unchecked them for a reason!  Why are they coming back?  I posted about this before, but all I was met with "that is default behavior, no problem to see here".  I hope the new team will look into this.
 



 
Problem #2:
 
With the situation above, when exporting my track to audio, it seems like Sonar doesn't recognize the input echo is enabled as in this setup above, any tracks that are getting its MIDI information from another track do not get their audio printed into the exported track.   So in this instance, I have the whole song, but not the bass line because the bass line's MIDI input is coming from Notemapper.   It seems like it is ignoring the fact that input echo is on.... yet it plays fine in the project... but exporting it doesn't work.
 
 
Again, I hope the new team can take a look into these more than decade old MIDI bugs.
 
Thanks,
Adam

1. If you add or delete MIDI devices (including virtual inputs and outputs) during your project composition or later when bouncing, the MIDI sources can get screwed up.  It seems to remember them in numerical order and if you have added or deleted any and all the original ones are not present on subsequent versions of your project, it will confuse things.
 
2.  I could be wrong, and maybe I misunderstand, but I don't think input echo is relevant except when you are recording audio or MIDI and want to hear the audio.  I don't think it has any effect when you are bouncing or exporting.  Are you feeding hardware synths or softsynths when you are exporting?  I don't think you can use "export" when dealing with hardware synths.  You have to record the actual audio first.
 
Maybe your Notemapper is confusing things?  Why not just separately record the two different bass tracks on separate audio tracks and then bounce them together to a single track if you want them blended on one track.

There is a long thread fro 2017 "Long standing midi issues with sonar" that might be worth visiting for your problem. I have not been helped, but I am still going thru several suggestions before I pull all of my hair out. I have been without midi in sonar for weeks now! Works fine in stand alone versions.
 
My own post "MIDI PROBLEMS..." has not provided any help.

My guess is this is because Notemapper gets loaded later in the project load process, and SONAR has already enabled the physical MIDI input on any tracks that are set to echo a Notemapper port, because that port isn't available yet. Not sure if that's par for the course with MIDI Out VSTs or is peculiar to Notemapper. Would have to test. More surprising to me is that your screenshot shows both Impact LX49 and MIDIIN2 enabled. Is the controller connected by both MIDI DIN to an interface and USB direct from the keyboard? Also, is this based on an old project or template? I have some old projects created in some bad version of SONAR that had all input ports enabled without having an Input Preset selected. Normally that should not be possible.
 
As for the export issue. MIDI from virtual ports is going to be treated just like live/real-time input from a hardware port. In order to get those tracks included in the export, you'll have to disable Fast Bounce and enable Live Input.

no its not that.  Even if I insert a new softsynth, it will get the MIDI from Notemapper because "Omni" is always the default.  I have to always select my MIDI keyboard so it doesn't get MIDI out info from Notemapper or other softsynths.

Why would cakewalk's initial setting be default?  Seems stupid.

There's a lot of default settings that are not perfect, Like, MIDI buffer is way to low, and the one that drives me nuts and has wasted more time then I can count is the default to comping when what I need is overwrite. 
 
Anyhow, I don't see why your using this method anyhoo. It is soooo easy just to clone the midi track. Your going to need the 2 instrument tracks anyhow so it's not like it's taking up track view space.  When you clone a track all further edits are duplicated to both tracks. If you don't desire that then you Copy the midi track. 
 
I think your trying to do things in a way that the developers did not count on so it's an uphill battle. 
I duplicate midi tracks all the time, for 20 years possibly, and it's a simple concept. 
In my minds eye input is only used for the recording of new tracks. Mixing is all about the outputs. 
 
And I like all my instruments in view and colour coded and labeled. If I double a bass part they will both be Blue, but I need the labels and the track and console view GUI goodies so I can mix to taste. 

i do this because I play it live, and want to hear all 3 layers of my sound at the same time.  And if I want to edit a note afterwards, i want to edit it once, not edit it on 3 different tracks.

As I said, if you use the CLONE TRACK to make a second copy you will be able to edit one track and the other 2 will also be edited. 
To hear the 3 instruments you simply select your controller as the input for each track and turn on input echo. This would seem to be the normal way people work. 
 
Example:
 
Insert either 3 simple instrument tracks or ( my preference) 3 midi tracks pointed at 3 VST instrument tracks. 
All 3 tracks will have your controller set as the input device. 
In put echo on all tracks. 
Now record this way only using one track to capture the performance. 
Now clone this track to the other two
All edits will be global. 
 
 

OK when I get back to my DAW I will try this.  
 
So when you clone a track, any midi changes you make afterward happen all the others automatically?
 
Thank You!