Are you saying that you switched the midi chip in your Herbert?
The chip in the Herbert should not effect your ability to use any midi footswitch. Then, depending on your footswitch, you should be able to switch effects on the Eleven Rack and channels on the Herbert. If your footswitch is capable of switching effects via IA, independent access, then you can switch effects on/off with individual button presses, aside from preset options.
Regardless, with any midi footswitch you should be able to switch presets on the Eleven rack and channels /presets on Herbert via your midi footswitch.
It is a KILLER way to run the Herbert. I have been doing it for a couple years and it is truly the bst set-up I have ever had.
Hope that helps.