I didn't receive an e-mail from them. I cannot think of a way to retrieve the reference number. Did you try calling them?
AFAIK, there is no communication from the consulate for any of the above matters. It is upto the applicant to pro-actively follow up the procedure and status tracking of each individual consulates as the process may vary. Now coming to this situation, I had couple of issues with 1. entering incorrect expiry date of passport
2. Not printing 2 sets since my printer had a paper jam and there was no way out.
I could use the reprint but it was of no use since there is no way to correct info already entered. I went ahead and created another registration and used this to get my OCI approved. No issues. Your previous registration is not even looked at. They only match your paperwork with the ones you submit with the application. If I query the status of the unsubmitted registration, it still shows "Not Acknowledged".
HTH