JS file reverts back to the source generated by Cocos2D-x when compiled on Eclipse

I encountered a problem when I Click run in eclipse. The project is built successfully but the file myApp.js is reverted back to the source existed when first generated the project sometimes it shows a yes/no dialog:

The file has been changed on the file system

Sometimes it just changes after build finished. and the apk file is still containing the first code generated by cocos2d-x, the hello world source code. I then tried modifying the file myApp.js with JavaScript editor and text editor, but no changes.

I’m working with :

Eclipse Android Developer Tools Build: v22.6.2-1085508
Android Sdk Manager Revision 22.6.2
Android NDK R9C
Cocos2D-X 2.2.2

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