When you make any changes in car wiring you should disconnect car battery to prevent shortcut.
I swaped my EWS II with battery connected(I forgot) and no problem.
To switch key chip you don't have to connect/disconnect any car/key battery.
You don't have to do any resets. Switch EWS II, key chip, connect battery(if not connected) an should work, unless you fried EWS II box