I am not sure if this is a DOS problem,Windows or Hardware
I just installed a new C drive. I have two HD 1 160g  (slave "D") and a new 200G primary(C) which I just installed.
after Installing the new drive DOS/Windows no longer recognizes the SECONDARY. It (DOS and Windows) both show only C drive. when I go to Bios or run any utility it shows both drives as drive 1 and 2. but when I load FDISK it says d drive is o and E is 1. these are my DVD\CD drives. but no SIGN of the other HD. ?   the system is:
Windows 98SE 4.10.2222a
INTEL DG845GVSR MB  with Intel Celeron  2g chip
 Custom-built machine two hd 1 MAXTOR 2O0G 1 MAXTOR 160G
Regularly run Adaware,Sbot S&D have AVG 7.5  anti virus
I have a Original WINDOWS 98SE CD Was the 160GB HD your former primary HD?  If so, did you change jumper settings on it to make it slave when you installed the new HD?  And, are jumpers on the new drive set for master or Cable Select?  Are both drives on the same data cable?  Some drives ship from the factory un-formatted....Windows will not recognise it until you format it.
Use the Utility CD that shipped with it to do this or DLoad and run the software from the drive manuf. website....