HELP! HOW DO I RECOVER MY INSTALLOUS APPS THAT WERE LOST WHEN SYNCING MY IPOD TOUCH?

PLEASE HELP! I have an Ipod touch version 4.0 model MB528LL and I believe its second generation. Anyway it is jail broken and i had a lot of games on my it including FInal Fantasy III. Then when i synced my ipod touch they all disappeared! I haven't unplugged my Ipod Touch or touched or messed with anything. So i was wondering if there is anyway can get those apps back and how do I prevent this from happening again?