triple posted.
the operators guide does cover this, i guess you lost yours?
i posted the toy link to the free manual, get it ,as in 2015 it drops off the chapter on security, chapter 1,, page 33 clearly states
what to do with the battery pulled. i sent the link in another post.
i click doors and locks.
here
http://www.toyota.com/owners/web/pages/resources/owners-manuals
then i click to page 33 see
BATTERY? disconnected?
it is there now or was, but life downloaded opr guides
are always better than 7 year old guides.(paper or not)
now ill paste it.
f the battery becomes discharged dueto the vehicle being unused for a long
time, etc.,
when the battery is recharged
or replaced, the system will give the
alarm. If this happens, immediately unlock
any of the side doors or back door with
the key or the wireless remote control
transmitter, and the alarm will stop.
reading further it does tell you how it auto arms
and auto unarms, key in ignition does disarm it.
and shows the key battery reset rules.
RTM its all there, unlike your post implies.