if you check form 1276 question no 73 asking you what visa you applying for.
And dont worry migration people can check your details with your passport number (also in form 1276 somewhere asks you what visa you are on now)
I had the same situation, immi account wouldn't let me apply online saying 'i dont not hold ?????? something like that'. then called to skilled migration people they advised me to apply by Email and advised to complete form 1276, attach all related docs. and I am also told to send a print screen (in my case i was getting message on the half way when i was applying online on immi) so i took a photo or print screen (a button on laptop keyboard called prtsc when you press that button it will take a photo of your screen) and attached with the email.
but after couple of days i was checking the receipt which i recived when i applied for 489, found they my first name +surname and again frist name (like frist name A and last name B they put ABA) when i tried the same name in immi ac my file took a step forward and i was able to submit online. i am sharing this story may be you have the same issues just check the receipt not the acknowledgment (i mean when you applied for 489 you must have recieved acknowlegment and receipt.
if the issues is same apply by email, send them your application and attach all docs and must attach prtsc with your email.
okey in my email i mentioned the issue and also told them skilled migration people advised me to apply by email. hope this will help you
Thanks a lot karan for your input . In my case problem is i was secondary applicant during 489 and not main applicant and now i am applying as a main applicant.
so how you finally submit your application online or by email.