The steps I underwent:

1. I had installed Flex Builder 3 beta 2 (FB 3 beta 2) as a plugin on my Eclipse 3.2
2. Opened my Flex SWF Library projects inside of Flex Builder 3 beta 2
3. Selected Flex 3 M3 (Beta 2) SDK at the dialog (default value)
4. Flex Buidler 2 had given me the following error in my log file: (full error info skipped for the sake of text clarity)

java.lang.IllegalArgumentException: Attempted to beginRule: P/FlexLibrary, does not match outer scope rule: P/as3corelib
at com.adobe.flexbuilder.project.actionscript.internal.FlexProjectPreferences.setUpgradeFlexSDK
(FlexProjectPreferences.java:147)
at com.adobe.flexbuilder.project.actionscript.internal.ActionScriptProjectSettings$2.runInUIThread
(ActionScriptProjectSettings.java:285)

5. Nevertheless of the received error, I was able to compile ALL my Flex 2 based projects that relies on my Flex SWC Library projects in FB 3 Beta 2
6. Then I had reopened my plain Flex projects inside Flex Builder 2 again, because at the company we are using currently Flex Builder 2 for the production.
7. But Flex Builder 2 constantly had failed to recompile all Flex SWC Library projects that were previously opened at least once at FB 3 beta2.

My resolution to this issue was to delete manually a config file created by FB 3 beta 2 and located at each Flex SWC library project folder at the following path:

c:\workspace\\.settings\com.adobe.flexbuilder.project.prefs

Mine Flex 2 authored SWF is 19 levels deep in its full glory:

[sourcecode language="actionScript3"]_level0.index0.VBox5.GradientBox25.indexViewStack.
mainPage.contentPane.mainViewStack.customerViewStack.
presentationViewer.swf.FlexLoader396.instance458.sfiViewer.
bank.foreground.sa04d14eaa39b3fd.content.clip[/sourcecode]