There’s a known data loss bug when using Subclipse and performing a package rename refactoring that includes subpackages https://bugs.adobe.com/jira/browse/FB-24990.
Please go to the Subclipse download page http://subclipse.tigris.org/servlets/ProjectProcess?pageID=p4wYuA or simply use this update site http://subclipse.tigris.org/update_1.6.x to get the latest version of Subclipse.
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