Search Engine Issues with JavaScript

I’m researching optimization of Flash Websites and I came across this important snippet on Google’s help pages:

“Googlebot does not execute some types of JavaScript. So if your web page loads a Flash file via JavaScript, Google may not be aware of that Flash file, in which case it will not be indexed.”

Which leaves me to wonder if the AC_RunActiveContent.js file (needed to avoid the infamous IE issues) will leave my Flash sites out in the cold when it comes to being found by search engines, (Google in particular).

Does anyone have any insight on this issue?