I'm not sure if you misunderstand how jailbreak apps work, or if there is something more sinister here.
The applications and tweaks you install or purchase through Cydia do NOT get backed up or removed by iTunes ever. They are completely separate and do not interfere with the syncing process. If however, you have allowed iTunes to update or restore your iPad then you will lose everything to do with your jailbreak. It does not sound from your description as though that is what is happening.
The only apps that would get removed when you sync are pirated apps which you have illegally sourced. If that is the case, I suggest you read our rules quickly. They are linked in my sig. We do not support or condone piracy here, so you will get no additional help to resolve your problem if that is what it is...
