HI Sukhwinder,
I think, If your funtional users made modfication in tables/objects then SPDD window will be prompt during ADJUSTCHK_PRE.
If you made modification and SPDD window did not prompt then you can adjust to modified object after upgrade and you can do it with the help of funiontal and abaper. So, there is not issue if SPDD window did not prompt.
I am also upgradating EHP 6 and I faced some modification during this phase because funtional users and ABAPER had made some modification in tables/objects. so, I login on shadow system and made the modification.
Regards,