Do you have a Fat32 partition on your HD, put the rom there and cd to it.
I.E. I have win2k on main partition and my backup partition is a FAT32.
When i boot with my win98se cd it make my Fat32 parition C drive.
I just cd to C drive and flash from there. all files are on root directory "C:\" of my backup partition.
Rules of Thumb:
1. Beside your OS partition always have a backup partition to save data.
2. Backup partition is best format as FAT32 since most OS will be able to read FAT32. WHY? NTFS can't be read by other OS except NT types. Unix Part like Linux Ext2 can only be read by UNIX. But Linux, NT, and other OS can always read FAT32. FAT32 is faster than NTFS in benchmark too..