Can anyone with the full version of Nectar repro this issue? 
 
As a summary, automating the harmony bypass in Nectar doesn't seem to work properly, and behaves differently if the Nectar GUI is open vs. closed.
 
1.  Add Nectar (VST3) to an audio track
 
2.  Add an automation lane.  Select Harm:Bypass as the automation envelope (Harmony bypass.  The idea is to bypass during verse, add harmony during the chorus, for example.)
 
3.  Automate so that there are regions where the harmony is enabled, and others where it is disabled.
 
4.  Close the GUI for Nectar.  Play the project.  ISSUE1: automation is ignored.
 
5.  Open the GUI for Nectar.  Play the project.  ISSUE2: automation is now active, but audible pop during the transition from harmony enabled to disabled and vice-versa.
 
6.  Export the mix with GUI disabled:  No automation.
 
7.  Export the mix (fast bounce) with GUI open.  Watch GUI level meters and harmony automation indicator bounce around during the fast bounce (!) Automation works, but now the Nectar track is out of time with the rest of the project.  (No PDC or something?)
 
Not sure if this is a Nectar issue or a SONAR issue, but before I start sending in bug reports I thought I would see if anyone can repro.
 
Thanks,
 
John

X3E I assume?
Do you get the same with VST2?

Sorry I don't have the plugin but I'm sure others will comment shortly.

CakeAlexS
X3E I assume?
Do you get the same with VST2?

Sorry I don't have the plugin but I'm sure others will comment shortly.

Yes, X3E, thanks for the reminder, I updated my signature accordingly.
 
Since VST3 has been working well for me I never installed the VST2 version.  Of course there are any number of workarounds for this, and I got the functionality working a different way, but if it's a real bug I'd like to report it to Cakewalk and Izotope.
 
Thanks,
 
John

Well you might want to have a go at VST 2. If VST 2 works and VST3 doesn't it would lean towards a Sonar issue in my view. Well hopefully others might give you feedback here first...

I assume Nectar is fully patched up as well.

CakeAlexS
Well you might want to have a go at VST 2. If VST 2 works and VST3 doesn't it would lean towards a Sonar issue in my view. Well hopefully others might give you feedback here first...

I assume Nectar is fully patched up as well.

Yep, just double-checked and 2.02 is the latest version. If I get some time I'll try the VST2 version and see if it works, good suggestion, thanks.

Please do report to Cakewalk and Izotope and have the issue fixed (if it's indeed a bug) because I'm thinking of buying Nectar and Alloy in the near future. 

This is Nectar 2 Production Suite? I just tested all but the export functionality per the OP with that. Let me preface that I have not used the harmonizer much, and never automated it, as I typically clone tracks and use Melodyne Editor for this.
 
1) When closing the GUI, the automations held for me, same as when open (VST3 version)... but note #3 below.
2) Reopening the GUI did cause a "stutter" on playback... the "Pitch" module came on/off at the Harmonizer on/off points. ALL other modules were disabled for this test.
3) Automation of the Harmonizer was not "on/off" as I could still hear "residual" harmony with using the automation in the disabled state. I am unclear how the automation for this works, as in SONAR it reads "true" (disabled) and "false" (enabled).
4) I did not test the export functionality with this.
 
I agree with Jlien X in that an official bug report to both Cakewalk and iZotope would be warranted. I can "sort of" verify the OP, but a "fix" lies with them.
 
Edit: Grammar

mettelus
 
1) When closing the GUI, the automations held for me, same as when open (VST3 version)... but note #3 below.
2) Reopening the GUI did cause a "stutter" on playback... the "Pitch" module came on/off at the Harmonizer on/off points. ALL other modules were disabled for this test.
3) Automation of the Harmonizer was not "on/off" as I could still hear "residual" harmony with using the automation in the disabled state. I am unclear how the automation for this works, as in SONAR it reads "true" (disabled) and "false" (enabled).
4) I did not test the export functionality with this.

Thanks a lot for trying this.  I think I may have had the same issue, the "residual" harmony rather than the harmony being disabled completely.  
 
I also use Melodyne or actual harmonies for final mixes, but for quick demos this method seemed promising.  I will file a bug report with both parties.
 
John

CWBRN-27299 reported to Cakewalk
#KVL-22474-332 reported to Izotope

Not a problem. This actually got me to look at the harmonizer more, which actually has some slick features in it (and definitely quicker).

I am not at my computer, so not sure if the main signal can be muted? I would prefer to use this feature as I do Melodyne, i.e. clone the vocal and cut all but the harmonized portions of the track. This "may" be a potential workaround, but muting that main signal would be necessary to be effective.