I am dovetailing into this post as I was trying to describe the same kind of problem on another post concerning scene builder, which as yet is unresolved. I am glad in a way to find that I am not alone in this issue.
In my humble opinion, there is something amiss with the scene builder functionality.
The way it currently functions, generating effects for a scene seems to be an all or nothing proposition. You cannot apply effects to one type of fixture, like tripars and generate the effect for the scene and expect to make changes to other fixture styles in the same scene either separately in the editor window or going back into the scene builder window.
For example, I wanted to put effects on a group of LED pars and separately make adjustments to scanners. Can't do it in the same scene. Or let's just say I forgot to add an effect on just one of 15 fixtures. Well, tough luck. Just expect to delete the scene and start over. One shot to generate all the effects for a scene. That's it. You can't edit your effects in a scene once you make the scene.
I wanted to do effects on LED pars and set scanners for no effects, just shutter, position and color. Sorry...can't do it. I found a really dumb work around that kind of worked. I created effects for the LED's and then did position effects for the scanners...but since I didn't really want them moving, I used a two-point scan profile and merged the two points together in the graph so the scanner thought it didn't have to move. Yeah, really useful.
I hope a fix is in play for the software. The effects generator is capable of some great treatments, but the current limitations in editing functionality is discouraging.