Hid settings seem to be being saved with the lens. Just hide some busses, saved the project and reopened. Busses were hdden. repeated but saved the lens, and when it opened, they were hidden.
 
I repeated with un-hidding the busses too, and it was the same.
 
Funny it's saved with the lenses, I still don't fully get them.

Okay, thanks for that. I guess it's a bug, as there is repeatedly one track - the same each time - that doesn't show the colour header. Perhaps that folder has become corrupted? 
I've tried saving the lens for the project after hiding the buses. I'll report back if it's worked. 

I don't think the folder is corrupted, because it still knows it's colour. But Sonar isn't picking it up for some reason when it opens.
 
Definitely a bug

Another workaround to changing themes to restore the Folder Colours it just to click on it to open the colours dialog box and close the box without making a selection. It then remembers what it should be set too,
 
One of my folders wasn't responding to this. It's latest folder in the project. remembering that I had  saved the scene earlier, and without a colour selection being set to this folder. I tried again saving the scene after setting the folder colour. And now the folder behaves like the other. Opens without a colour, but can be recalled by changing the theme, or opening and closeing the colour dialog box and not making a selection.
 
Seems Scenes is connected to this.

Kamikaze
Another workaround to changing themes to restore the Folder Colours it just to click on it to open the colours dialog box and close the box without making a selection. It then remembers what it should be set too,
 
One of my folders wasn't responding to this. It's latest folder in the project. remembering that I had  saved the scene earlier, and without a colour selection being set to this folder. I tried again saving the scene after setting the folder colour. And now the folder behaves like the other. Opens without a colour, but can be recalled by changing the theme, or opening and closeing the colour dialog box and not making a selection.
 
Seems Scenes is connected to this.

thanks for the workaround tip Kamikaze. I'll try it out...weird little bug.