Success! Looks like we've fixed this one. According to our records the fix was applied for
a recent build.
Designer 2.0.0 Beta Build: 276 (Duplicating Store Issue)
Designer Version Tested: Sencha Designer 2.0.0 rev 276
Operating System: Windows 7 Professional x64
Framework: Ext JS 4.x
Description: When duplicating an existing array store from within designer, the designer.js file within the deployment folder does not update the stores array to show the new store.
Workaround: Do not duplicate a store, simply recreate it.
Thanks for the bug report. Another workaround that may be quicker than what you've suggested above is to duplicate it but go into the Application node and add the new store in the store configuration.
This is fixed in the next auto update (after 288).