Invalid system disk, press any key

I have a asus k7 motherboard, amd 750 processor,SB live soundcard, 3dfx 16mb video card, 2 operating systems(win 98, 2000) on a 30 GB 7200 rpm hard drive. Fat 32 file system. I received the ” invalid system disk, press any key to continue” error after running Norton Systemworks 2001 optimization wizard. This is the second time this has happened to my hard drive. Lasttime, i fixed it by using Sys c: and recovered win 98 but lost my win 2000 partition. Now, I am able to get into my win 2000 partition but not win 98. Any fixes besides re-installing win 98? Can i replace the command.com file?