It used to be that CIC administrative error could qualify an applicant for urgent processing, but it looks like this has been removed:
http://www.cic.gc.ca/english/citizenship/become-urgent.asp
Regardless, I recommend that you contact your MP to register your frustration and see if they can encourage the CIC to find your first application, or barring that, put some extra care into timely processing of your next application. This may or may not work, but it's important for the CIC to have some level of accountability.
Also, include a cover letter noting that you are resubmitting due to CIC administrative error (loss of application submitted date XX) and include a photocopy of the CIC delivery notification of your previous application. Notethe advice of the Call Centre employee named XXXX and consulted with on this date: XXXX. Applicants are not allowed to have more than one citizenship application at the same time, so you want to show that you've done everything right and that it was CIC that made the error in case your previous application is found and the CIC both applications in process.