I have a couple of ideas that may help:
#1 - How would you handle this with your original system? Would you have people turning in lists of who had checked in? In that case, you wouldn't have a list of who had checked out. Would you look at the lists in each room as you rounded up kids? Do the kids ever change rooms without something being recorded? To which location would the children evacuate? Could it be a location on campus where there is still a PC with access or perhaps near one with the printout of the daily activity? I don't really have any good ideas on this one, but there may be other things to think about here for emergency situations.
#2 - Would Tag Comments work here? If not, is it because there isn't enough space? Those comments are designed to be on the tags for each child and I've usually seen them used for allergies and similar.
#3 - no real ideas on this one. Perhaps add a parental cell phone # to the tag comment? I've seen that being used in a more common manner with more and more parents having a cell phone. Our church has pretty much ditched the pagers because of that. (Our pastor loves this :-) )
I would like to see what others are doing in this area as well. I'm sure that someone must have addressed these concerns before and they'll be around no matter what system is used. You've also given me something to think about for our own children's ministry.
In Him,
-Peter Schott