Hello Naveen,
SPDD and SPAU activity would highlight the list of objects that has the deviation.
1. Please check with your team if there is any instance where you had added includes into FORM ROUTINE userexits with an SAP key. SPAU or SPDD wouldn't be able to catch such difference for the manually added modifications and you need to add them back again.
2. Once the system is upgraded, please run the basic testing to ensure there are no short dumps, CIF queue errors etc.,
Hope this helps.
Thanks & Best Regards,
Babu Kilari