Error: The client you transmitted is not associated with the agent number you supplied and cannot be authorised. 

Solution: Please check your client list on the ATO portal if the client with error is still recorded there as your client. Because this error will not show, if this client is in your ATO portal before lodging the return.  Also, please check if the ABN and TFN of client are valid. 

If ABN or TFN is invalid, please check on ATO portal the status of lodged form. If it's not lodged, please contact ATO to get the instructions, if they can fix the TFN and ABN of lodged form online. If it won't help, please let us know  and we'll contact ATO tech team for them to investigate it.
LodgeiT never changes user's data or forms automatically, only users can do that manually .  Also, LodgeiT doesn't have the permission to access ATO agent's client list, therefore lodgment cannot affect contact.