Had a similar situation 3 years ago. Submitted 2 applications. Never got my SMS.

Went to the SAPS station often to get my ref number. Got told to be patient. After 3 months I went there again and was told as I walked into the DFO office, Mr F... don't worry, your applications are at Provincial or CFR. I said great, just give me the ref numbers.....oops, one got lost.
DFO asked me if I made a copy and asked if I can quickly bring it in. 5 minutes after processing and fingerprints, I got my SMS. Was promised that the re-submitted one will be approved before the other one, which then did happen.

Always keep a copy!