At this stage, you flipped both the labels of the electrodes AND the channels of data. This was necessary to find a solution to allow moving the order of the channels in the ERP file.
But indeed, if you stop here, it produces the same topographies as before.
I think that the only last step that you need is to replace the "flipped" channel file with the original channel file, and you would obtain a flipped topography, that you can average/compare with the non-flipped ERPs.
Maybe there was a simpler solution to do that from the interface.
Scripting it in Matlab, as suggested above, would have been relatively easy I think.