I do not know Flex Builder project config files (I do know very well ClearCase though), but this question looks like "Do you keep your project files under version control ?" or "Which eclipse files belong under Version Control"
In essence, you should put any config file in ClearCase as long as you have relative path and/or variable for the other users to interpret.
A snapshot or dynamic ClearCase view will simply present those files for them to use, whatever they are. For instance, some eclipse .project or .classpath can be stored that way, while using linked directories.
So for Flex Builder project, one way to determine what file to store is to copy a minimal subset of those files in a new directory and check if you can re-open your project successfully.
Once the minimal set of file is determined, you can "add to source control" them.