Yes, calling the (departure airport) Center Flight Data to get the three digit "CID" number and having the crew quote this to Clearance Delivery normally works if Clearance say they do not have a plan in the system. It could also be that they are requesting clearance too early - I think that 10 minutes prior to planned departure time is the norm. Also, if a flight is delayed, the ATC filing can drop out of the system after either 90 minutes or 120 minutes depending on the Center if the departure time is not amended. Cleveland Center will drop flight plans after 90 minutes for example, whereas in Minneapolis Center, it is 120 minutes.