Ricebug
It appears that the HE plugin is taking input from ALL the MIDI tracks in the song, not just the one with the chords.

Did you try using the MIDI Channels option?  To start you should re-assign any other MIDI tracks to channels other than 1,2,3, or 4.  Then depending on how complex your harmony is create a MIDI track for channels 1,2,3, or 4 each would play a single note of your harmony.  You need to select the Harmony Engine as the MIDI output on each track then the channels now show as 1: Harmony Engine x64 , 2: Harmony Engine x64, etc.  Based on what the manual says this is how it "should" work.  I have not tried this yet so.... best of luck!  Hope this helps.
 

Ok.  I just tried using MIDI Channels as I posted above and that worked for me.  I had a piano in an audio channel (bounced from Inst track using MIDI channel 5 so no conflicts later) with the Harmony Engine inserted, set it to MIDI Channels for the Harmony Control.  Created 3 MIDI tracks each set to output to the HE, and set to channels 1,2, and 3 respectively.  Recorded my individual harmony notes to each track.  It then played the original piano with the 3 harmony notes upon playback.
 
This is with the VST2 x64 version of the plug-in on Sonar Plat Cambridge.  My HE EVO version is 4.0.0.7 which I think is the latest.

SF_GreenDid you try using the MIDI Channels option?

This is where I lost my plugin. Everytime I tried changing it, the stupid plugin would put it into MIDI Chords mode when I hit playback. So I deleted everything associated with the HE plugin to start with a clean slate. However, when I re-started Sonar, I got the "missing plugin" error and then saw that it had been removed from the VST audio FX list in the browser.
When I rescan the plugins, Sonar sees it but it's still missing from the browser list.

Ricebug

SF_GreenDid you try using the MIDI Channels option?

This is where I lost my plugin. Everytime I tried changing it, the stupid plugin would put it into MIDI Chords mode when I hit playback. So I deleted everything associated with the HE plugin to start with a clean slate. However, when I re-started Sonar, I got the "missing plugin" error and then saw that it had been removed from the VST audio FX list in the browser.
When I rescan the plugins, Sonar sees it but it's still missing from the browser list.

Wow!  That sounds pretty messed up.  Don't know how to help you with that, sorry.

SF_Green
Hi mudgel, yes I did, but I've never gotten it to even show up in my VST3 list  (when showing "All Plug-ins").  Maybe this is the 'conflict' that Antares fessed up to Ricebug about.  Know any tricks to make that happen?

No tricks. The last update that Antares did was supposed to address Sonar issues and it just installed and worked fine. This was a while coming though and there were lots of probs when AVOX 4 first came out! So I haven't used it much. Now I use iZoptope's Nectar 2.

Here's a response from Antares on how to rig the Harmony Engine for Sonar:
 
Hi Terry.
It is a little bit tricky to do this in Sonar. You will first need to configure Harmony Engine as a VSTi plugin. Here’s how to do that: 
1. Open Sonar
2. In "Utilities," choose "Cakewalk Plug-In Manager."
3. Harmony Engine EVO will be found under the "VST Audio Effects" the left hand "Plug-In Categories."
4. Please highlight "Harmony Engine."
5. Under the "VST Configuration," (in the lower middle of the "Cakewalk Plug-in Manager") click "Plug-in Properties."
6. In the "VST Plug-in Properties" window, choose "Configure as synth."
7. Click "OK."
8. Harmony Engine will now appear under the "VST Instruments (VSTi)" in the "Plug-In Categories."
9. Click "Close" to close the "Cakewalk Plug-in Manager."
10. Close and relaunch Sonar.
11. Harmony Engine will now be available as a VSTi insert.
12. On your audio track go to "insert soft synth” and choose Harmony Engine.
13. Create a midi track and set it’s output to Harmony Engine.
 
Matt Antares
Audio Technologies
 
FYI for everyone, I was able to get the plugin back by a simple reinstall of the plugin and a reset/rescan within the Cakewalk Plugin Manager.
 

Ricebug... yes you can do it the way Matt says, which is what my neighbor, SF green said... but its now easier by doing it as others have suggested.
 
It works fine here also... mucked around a bit last night...multiple instances, no probs...
 
Hey, Mike... yea, I enjoyed the Nectar 2 system while I demoed it over the holidays thinking bout the super deal on the bundle...but ended up going all FAB instead.... Glad I did!
 
Quite frankly, they all suck...both sounded very synthetic... nuttin' like the real thing! Maybe as a backdrop for "big" harmonies, behind several real ones... I'll have to try that!

VastmanQuite frankly, they all suck...both sounded very synthetic... nuttin' like the real thing! Maybe as a backdrop for "big" harmonies, behind several real ones... I'll have to try that!

True. I typically layer real harmonies over synthetic ones, giving them a nice, fat sound.


Also, you can copy a vocal, and raise/lower it in Melodyne Essential. Then, with some judicious use of the formant control, get rid of the chipmunk and robot sound.
 
Another trick is to have a MIDI melody of the harmony parts sent individually to the singer's headphones. After a bit of practice, they should be able to accurately track and sing along with the MIDI track, giving you a decent harmony voice. Depending on the part, you may have to raise or lower the pitch if they can't sing that high or low.

They're all bits of kit. They all come in handy sometime, somewhere. In the past when I was still working, if it was profitable, I would buy a plugin just to do a single job.

I have been getting great results layering Harmony EVO harmonies behind vocal tracks mainly using Chord mode. I find using AUX tracks great for this as you can record multiple variations of EVO harmony outputs onto separate AUX tracks and create enormous sounding vocal harmonies without much CPU impact.
 
For songs where there are only a few chords I found that I can select the chords "on the fly" as the song is playing but I have also been experimenting with automation for more complex songs and it kind of works but I can't get my head around how Cakewalk displays the results. The results are displayed as lines with nodes just like they would be for, say, volume automation. Works fine for volume - I can understand how the line equates to volume, but I don't get how it equates to selection of a specific chord button in the harmony preset block. Consequently, where it has recorded the automation incorrectly I cannot see how to edit/correct the automation. The chord buttons are shown as, for example, H Button 1 1 or 1 2 (row 1 col 2) in different colours but I cannot see how to change these or even add them from scratch (rather than recording them) so that I can create the correct sequence of chord changes. 
 
Can anyone please explain how to do this in Sonar?
 
Thanks in advance