Hi Vij,
The first activity to be done in SPAU is Note Correction before doing with/without modification assistant. It will display all the sap notes implemented in earlier version. Most of the notes becomes absolute in new version.
Check the implementation status of the note by clicking on note number. If it is "can be implemented" need to implement and execute as per the steps.
If it is "Cannot be implemented", it becomes absolute in new version. Click the traffic lights and reset.
Please find below links for more info.
Download SPDD and SPAU Adjustments Handbook from the below link.
Regards,
Varma