If the battery was gone you wouldn't be able to set up and install Windows on the older drive. The first thing that would be seen when first powering on the system would be the first bios setup screen for time and date settings. It sounds more like a damaged "MBR"(master boot record) or loss of partition information. With a boot floppy if you are running 98 or ME you would type in "fdisk /mbr" at the dos prompt and press enter.
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