Time only passes when you're actually in the garden, so if they died, you'd have had to have been present when it happened. Most likely, you didn't save properly. However, if you want to make sure, check the Chao Transporter - go to Move, and you'll be able to view all your chao in each garden (if they're in a lesson they'll have an X over their image). If your chao doesn't appear on there, it's gone.
~ Crazy C Lea