You have to understand HOW family tables work. Only the generic file actually exists. There are shared features/dimensions between the generic and instances. When only the generic is in session and you make a change then only the generic has to regen. At that point if you were to go into the FT editor and check the table validation you would most likely see that the instances are NOW listed as unverified. Again, this goes back to how FT's work, when you are looking at or using an instance it must first regen the generic then apply any differences in the features or dims. to get the finished geometry of the instance. That's what the validation does, it opens the instance without graphics, applies those changes and makes sure that the regen doesn't fail. So you said that you validate but first that is gone once you make a change to the generic and second, validate just makes sure that the instance doesn't fail it doesn't save that geometry.
Let me step back to how you are using the FT part in the assembly. From your description it appears that you are using both instances in the assembly. Because of this the assembly is going to require that the instances are both up to date and fully regenerated. So that answers that the part about why the generic and both instances need to regenerate if you make a change to the generic. This is why the instance accelerator isn't helping either. It would help when you OPEN the instance but doesn't prevent the instance from needing to regenerate when the generic is modified.
Now to your main question, how to prevent this from happening. You don't mention if you are using Windchill but if you are you could TRY locking the instances in the workspace or setting them to be Read Only in Creo. I'm not at all sure if this will work but it's the only thing I can think of that MIGHT help. Finally, this is one reason that FT needs to be used with care. A 1000 feature part might not be the best use of FT. It might have worked during development because you can save time by having 1 modification affect multiple parts but if you're that far down the path it might be better to split them from the FT.
