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

Solution: Please check your client list on the ATO portal and this client is still recorded there as your client before you lodge the tax return? Because this error will not show if this client is in your ATO portal before lodging the return.

LodgeiT never changes user's data or forms automatically, only users manually can do that.  Also, LodgeiT doesn't have the permission to access ATO agent's client list, therefore lodgment cannot affect contact.