No changing the gearbox will not affect the EWS. And for that matter 328 are running EWS II which is not possible to by pass compared to the EWS I of the 325 and below.
There is a method but that involves soldering work.
If you mean EGS then it is partially wrong as well. between the 4speed gm and 5 speed ZF they will share the same EGS.
Only the Jatco will use a separate EGS from the EURO gearboxs.
Reason is the Jatco is Japanese. it doesn't understand german so have to use a Japanese speaking CPU to talk to it.
EGS for GM and ZF GB
http://www.realoem.com/bmw/showparts.do?model=CD22&mospid=47447&btnr=24_0955&hg=24&fg=20
GM is A4S 310R
ZF is A5S 310Z
EGS for Jatco
http://www.realoem.com/bmw/showparts.do?model=CD22&mospid=47447&btnr=24_0957&hg=24&fg=20
A5S 300J