Question: The initial CTR lodged were showing as missing due to incorrect TFN. But after I corrected the TFN and lodged again, they were still showing as missing.

Answer: 

Response from ATO, please see below: "When a software user makes a mistake and enters the wrong tfn, this means that the return will potentially be lodged under the incorrect entity. In the case where the tfn is valid, it means that the return will be in a state of 'suspended' because the ATO systems take the TFN as the identifier under which to lodge the return. If the TFN belongs to a different entity type from the return completed (i.e. if the TFN belongs to an individual and the return type is for a company) ATO systems suspend the return and may transfer the return to the correct entity or cancel it (depending on exactly what issues are present). In this case, because the agent lodged again as an amendment, there was no original for the company on ATO systems (under that client record) because the return was suspended elsewhere in the system.

In these cases, the agent should call the ATO and report what they have done and ask for the return to be transferred across to the correct entity. They can call the agent number or https://www.ato.gov.au/Tax-professionals/Support-and-communication/phone-services/tax-agent-phone-services-(fast-key-code)-guide/
and request this be actioned. The agent can call to cancel the most recently lodged returns, however if all the information is the same this should happen as part of the process (they may be contacted by ATO to confirm)."
Please let the user contact ATO directly and explain the issue, they should provide further instructions. Please let us know the progress.