There is a TSB on the Hyundai Tech site  http://www.hmaservice.com/index.jsp
on how to reprogram your system, depending on what type you have.  When you
find it, in the ELECTRICAL TSB area, then under SECURITY SYSEM RESET, print
it off for the Hyundai people.  My very brief read leads me to believe you
will need a programmer to reset things.

You can search around there for the problems about your tranny too.
(another post by you?)  There are lots of tranny bulletins for the Hyundai
tech to refer to, depending on your symptoms.  Sounds like they are too lazy
to check them out themselves.

Good luck