Has anyone else noticed midi parts and instruments changing tracks since the latest update to Sonar? It's totally ruined hours worth of work for me. Save project, everything fine, go back to work on it and even though visually my midi part is say on track 3 the part is actually playing on track 2. Seems only way to sort it out is to create a new track with the instrument and re-build the sound and effects chain.

I had a similar problem a few weeks ago. I had a small project I had set up just to check that all my updated A|A|S instruments worked ok.

I had five synths on the go which I had inserted as a MIDI and associated audio track.

Then at some point the MIDI tracks all switched their association so that when I made my Chromaphone MIDI track active it played Ultra Analog instead.

Had me scratching my head for a bit...

When it first happened I manually reset all the output associations to the correct synth. The next time it happened I closed and reopened the project and all was okay again.

Then I went on a ten day break and when I returned 2017.09 was released and since that update it hasn't happened again.

Like Synkrotron I have seen an issue with midi being reassigned in recent updates. Always seemed to be related to track deletion, where after deletion midi would be reassigned in other tracks. Would be good news indeed if resolved in 09 release.
PIA but not a show stopper here.

I have experienced a similar thing in the past as well - in my case it was that if I had a MIDI track whose input was set to a synth with MIDI-out enabled, and then I inserted another synth with MIDI-out enabled into the synth rack, deleting that 2nd synth would cause the input of the MIDI track to change to the previous synth in the input list. A weird problem that's slightly different to yours but maybe related.  

It's weird I only noticed this happening after upgrading to the 08 version, pretty sure nothing has changed in my workflow although I have started using a MIDI out to external synth recently so Sharke you may be on to something there.
 
Going to update to 09 now.
 
Thanks for the tips and at least I'm not alone on this.