Noel Borthwick [Cakewalk]
If someone can build a really simple project with some mix scenes that demonstrate the issue I can try and look into it or work around it. 

In the case of Replika, it's pretty easy.  Just set up two scenes on a very simple project, one scene with Replika on a track and the other without.  Any changes done to Replika are lost when you come back after a scene switch, if the scene is saved or not before switching.  If the changes in Replika are first saved to a preset before switching, then  the setting will be 'remembered'.

And you can also very easily reproduce the issue by using Voxengo's free plugins (I used Stereo Touch, Tube Amp, and Sound Delay in this test).
 
1. Select whatever factory preset you like from the GUI's Preset-->Factory ROM drop-down.
2. Save a new scene.
3. Reload the scene.
 
The settings are back to the default.

stevec
I swear when I made a single change in Valhalla Plate as the only change before saving a new mix scene that change was lost, but as soon as I started making additional changes (those two plugins or otherwise) and re-saved the existing mix scenes the changes were retained.  

I found that I was getting unexpected results because I had the setting checked to automatically save when switching scenes.  That doesn't sound like your problem but I thought I should mention it in case others are tripped up by this.
 
The work flow I was using was to explicitly save the changes to scenes right after I made a tweak I wanted to keep.  And if I didn't want to keep that change, I would just cal up another scene.  But it doesn't work that way if you have that setting checked.

Indeed - I find the autosave setting can lead to unexpected behavior if you aren't careful.
I find it more predictable to explicitly save when I choose to.

cparmerlee
I found that I was getting unexpected results because I had the setting checked to automatically save when switching scenes.  That doesn't sound like your problem but I thought I should mention it in case others are tripped up by this.

 
Thanks for the tip, I didn't know about this setting.  In my case it's On so I've been saving for nothing prior to switching, but the settings are lost just the same.
 

The work flow I was using was to explicitly save the changes to scenes right after I made a tweak I wanted to keep.  And if I didn't want to keep that change, I would just cal up another scene.  But it doesn't work that way if you have that setting checked.

Interesting use of mix recall as an extensive undo feature.  I'm not sure now which I prefer, but I tend towards the autosave.