Follow up to my last post. I am having to do this enough that I wrote a bat file for it. Here is what it looks like if anyone is interested. Just copy and paste the code below into a notepad and save as a .bat file. I put mine in the root of my C: drive so I can simple do Start-->Run-->fix_content_assist.bat
fix_content_assist.bat
@echo off
REM The following will delete the prefs file in Flash Builder 4 Beta 2 that caused content assist to break
RMDIR C:\work\dev\morphic\myproject\trunk\code\as_fb4\.metadata\.plugins\com.adobe.flexbuilder.codemodel /s /q