no it is not possible to do that. there are apps that make lists of what apps you had installed the re installs it when you jailbreak but you cant put it in itunes to backup in any way
so if i am only looking to add mp3s to my playlist or the gym there is no way of doing so without having itunes remove any jailbroken apps that are installed?
It's not the jailbroken apps that iTunes is removing it's the cracked apps that you've illegally downloaded. iTunes can't remove jailbroken apps you've downloaded from cydia because iTunes can't recognise jailbreaks.
If you don't want iTunes to remove those apps then buy them from the app store...
i am in cambridge atm also ;p on milton road here for work
but the website rules are not to talk about cracked apps or how to... thats why gaz is saying buy the apps instead of telling him how to do steal them and be able to sync it with itunes