v2017.03
For a few days I had the problem, that after a "Rescan" of the vst-plugins all my simple-instrument-tracks are assigned to the false synthesizers and instruments. But now I see, the problem has a different cause.
It is because I enabled (at the same time) external MIDI-Outputs to external synthesizers.
- Novation Bass Station
- Roland Integra 7

And now all simple-instruments are again routed to an other plugin and to an other track.

For example:
When I solo Track 7 (AKAI VIP - vst-synthesizers), it plays the notes from track 9.  ! No Joke !
And when I click on the keyboard-icon (in the track-view) it opens "Kontakt" istead the AKAI-plugin.
But what I hear is the AKAI VIP synthesizer - not the Kontakt - with the notes from the false track.
When I select other extern MIDI-Outputs and MIDI-Inputs I get again a different assigment.

That is no joke.

Is there anyone else who has the same problem ?
Is the problem only with the simple-instruments?
Is the problem the order of MIDI-out and MIDI-in ?
How can I prevent this?

I don't have any VST Instruments/MIDI tracks.  But my "analog" tracks and VST plug-ins are OK.  I can open a project made with an earlier version of Sonar and everything is still intact.  

The audio-tracks and all other vst-plugins are also intact.
Older projects from 2016, 2015 and older open with the right instrument-plugins at the right place with the right midi-track.
Affected are my 2 projects that I startet with v2017.03 or 2017.02 (I'm not sure)
 

Not seeing it here, but I always use separate MIDI/audio tracks, never instrument tracks. Could be specific to instrument tracks, or it's a corrupt CWP file. Can you duplicate the problem in a fresh project?

Do you mean, when you select Insert>Soft Synth>'Whatever synth'>Simple Instrument tracks you get 'totally different synth'. Then yeah I've had this this month. I had made my own custom Plug In Layout for synths, and it was all screwed up.
 
I set it back to the Sonar default categories of Sort by Category/Manufacturer/Type, and it was fine.
 
I had planned on making a new layout, but after seeing your post and checking , it's working fine again. Maybe try the other plug in Layout choices for a bit, of make you own layout fr a bit.

I have had the problem occasionally. TBH I don't work with huge clusters of Soft instruments often. The last time it happened to me was when I played with orders and deleted soft synths. Somehow this mucked it up. My thinking then was if I had left it alone it wouldn't have happened.
 
We should be able to delete and move things around. All should be well so long as we didn't play with midi channels and inputs.

It happened as I enabled two MIDI-out and MIDI-in to extern synthesizers. At this moment no project was opened.
As I openend a project, where I just worked 15 minutes before, all simple-instrument-tracks are assigned to other midi-tracks and vst-instruments.
I try to reproduce it in a new project.
 

Is it consistently the same instruments that are swapped? I'm wondering if it might be a case of duplicate CLSIDs, are rare but not impossible occurrence.

"... enabled two MIDI-out and MIDI-in to extern synthesizers ..." Do you mean in Edit->Preferences MIDI devices or MIDI instruments, or do you mean enable input echo on tracks, or ???

I've seen this when opening legacy projects from time to time.  I don't use simple instrument tracks though.