Pre-comps are supposed to work this way. Notr sure what else you are looking for. Sometimes great things only come the hard way, so rather than getting strung up on this and wasting lots of time looking for solutions simply bite the sour apple and do things manually.
A pre-comp is just a comp. It becomes a source. What does not make sense about changing a source file and having it change all instances of that source in the project. It works like that for a photograph used in your project. Open the photograph in Photoshop and change it from color to black and white and all instances of that photograph in the project are not black and white.
It looks like you have a bunch of individual shape layers, one for each circle. What I would do is to add a bunch of ellipses to a single shape layer, animate that, then duplicate the shape layer and make your changes to the shape layer. This way you are not changing the source of the layer. Does that make sense.
Thank you RICK! that does make sense and makes it slightly easier to control the duplication/modification process
Ok I was quick to get excited...what did I do wrong here by following your example. I should've been a lot clearer in my pursuits...
the ellipse shapes animate in increments, they go from one to another.
So the very first shape moves moves off screen INTO the screen, followed by second, third, fourth, til the last...
when I follow your example Rick, from the very first keyframe I get all 9 shapes... instead of them animating..
What did I do wrong in keyframing the positions? I can't figure it out even by reorganizing...
Nevermind - I realize the effect I'm going for is best done with multiple shape layers such as before.
It's not clear what you did wrong from your screenshot because I can't see all the keyframes but, if I understand you correctly, you want to move each of the balls into the frame one at a time. That's easy. The timeline should look like this:
Here's a project file as a CS5.5. There's no need to put all 9 of your shapes on a separate layer.