Good Day
i May not Expert but cant understand your statement
1) Its a server running server 2003 with 2 drives mirrored via a SAS card.
2) Also the data on both drives do not match
if it is Raid1 both Drives Data has to be same Raid 1 is Mirror.
Solution:-
if you want to upgrade Hard Drive
A) Clone Os HDD to New HDD
B) Connect HDD to New Controller & Repair OS
C) for Server Password you can use Hiren's Bootable CD to Remove Password.
Don't Experiment on Original HDD
Good Luck.....