Yes, you can do all that..
I made a sample, although the scripting gets a bit complex but this should do everything you need:
http://ross.brickftp.com/f/597d3015b
It has widgets for controlling the rocks remainign, and when you decrement it, it will start an anim controller that blinks the rock. If you increase the widget, it will put the rocks back on.
You can animate the graphic on and off with a pause/reverse event like you describe and the rocks will come back to their correct state.
Play my sample back from the sequencer and adjust the widgets to see how it works. There are scripts on two different text objects (RedRocks, GreenRocks) that plays the anim controllers and resets the rocks. There is also a script on OnOnline that makes sure the rocks are in the correct on/off state when animating the graphic on.
There are 16 different anim controllers (one for each rock), but these aren't on the scene director. You'll find them in the animation controller tab on the right side.
Let me know if you have any questions.
Brian
#XPression