I had the CASA lost paperwork treatment. I submitted an application to reserve a registration mark. Got the automatic paperwork received, wait 2 weeks email. Waited 3 and sent an an email to see what was going on. No record of it in the system, can you please resend. So I send it off again but by that point supposedly the rego mark had been taken by someone else. To cover their tracks in their response letter the reference the data I had to resend it them and not the original date.
I now CC the DAS in all CASA correspondence no matter how mundane. I don't know if it helps but at least when they claim to have lost the paper work I can get them to check the boss's inbox.