I understand that you are concerned about applications being deleted, I can understand your concern that you may have. I would not want you to lose any of your applications. Please email me back and let me know what if any applications have been lost.
Reset iTunes and try to sync your iPod again, if any applications are lost please email me and let me know what ones were lost and I will let you re-download them for you.
If you have any further questions or concerns, please feel free to email me back.
Have a great night!
iTunes Store Customer Support