I ignore only the .settings directory.
You should look at the source of the project files ( .actionScriptProperties , .flexProperties , .project ) and decide whether you or your team need their settings during a clean check or not.
If you put these files in a version control, you should avoid certain directories on workstations in the settings (Flex server settings) and replace them with path variables .
This is, for example, the contents of my .flexProperties file:
<?xml version="1.0" encoding="UTF-8" standalone="no"?> <flexProperties enableServiceManager="false" flexServerFeatures="4" flexServerType="2" serverContextRoot="/myProject" serverRoot="${HTTP_DOCS}/myProject/" serverRootURL="http://localhost/myProject" toolCompile="true" useServerFlexSDK="false" version="1"/>
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