SSIS objects that use connection managers do so by the connection manager object GUID and not the name of the connection manager.
As a result when BIDS Helper's Reset GUIDs (or any other means of changing the connection manager's GUID value) is used object references are "specifically" coded to reference that package's connection manager.
For development productivity, if you subsequently copy and paste any SSIS object from one package to another after having previously setup connection managers using uniform names, all the pasted objects that contain references to these connection managers will produce an error "Connection manger {your GUID} does not exist. When opening an object with the error "Connection manger {your GUID} does not exist you will note that the Connection property value has a GUID rather than a named connection manager value.

Additionally, should you use SSIS variable's with property expressions to store your SQL, you will note that the varaible with the same name has no problem being referenced after performing the reset GUID.

The expected behavior in the scenario outlined would be that of all other SSIS objects, that is match based on object name not based on GUID.