I now do all my Flash development in Flex Builder 2. No exceptions. But I still use another installation of Eclipse for other types of development (ColdFusion, Java, HTML, JavaScript, etc.). Yesterday, I ran into a situation where I needed to embed a small Flex application in a custom HTML page, so tried installing CFEclipse into Flex Builder 2, and it seems to work perfectly. It’s not guaranteed to work, and I supposed it could break in the future, but for now, I’m a very happy developer.
Update: I should qualify that I’m talking about the standalone version of Flex Builder 2. The plugin version will definitely work with CFEclipse.