Hello.
To start with, let's make sure the two hard drives are not causing problems with each other. Although the BeOS recognizes both drives, there still may be some kind of conflict. This is based on practical experience, not on any theoretical ideas.
Now if both of these drives are IDE drives, and you have two IDE cables in the computer, we can try the following. Remove the cable from the CD-ROM drive. And while you're at it remove the power connector. not going to use the CD-ROM.
Now plug one drive into the first cable and plug the other drive into the second cable. The idea here is to have the cable for each drive, but we have no need to worry about the jumpers on the drives at this point. Now plug the machine back in to the wall plug and that turn on the power as usual. You should see a report that shows old has-been recognized. If not, given to the BIOS and try to select the drives manually. On most systems that means you have to set the options to auto.
at this point save the changes and exit. Notice what happens. If you still have problems, turn off the machine again, turn it back on and look in the BIOS.with each drive on its own cable BBI OS will have to find the drives. If it cannot find the drives even after two reboots, you've got something wrong.
But if the BeOS now recognizes both drives, yet the system will not boot, then we can go from there. I have a hunch that the drive jumpers were not configured properly for those two drives. Some older drives had strange jumper configurations that would make them not work well with the newer drives.
But trying to salvage a very old hard drive is not always a good idea. They don't perform very well, they may draw more power than they should, and they are not reliable. When you say old, I think you mean older than five years.
You can buy very good IDE drives today at bargain prices. So there is not too much reason to try to salvage a very old drive.