I'm trying to think what you could have done in the BIOS that messed up your drive. The BIOS settings only exist in there, so it should not have affected your drive at all. Nothing should have been deleted because of it. The main issue that could have happened is that you changed the drive settings. On those BIOSses you needed to set the Cylinders, Heads and Sectors for the drive you were using manually and if you changed something here, the drive will not be recognised anymore. If you're lucky, the BIOS will have an 'auto-detect' option in that section and you can click on that to find the needed numbers. If that option is not there, you will need to get the drive out of the computer (but you will be doing that anyway to copy files) and look on the drive itself for those numbers. Fill those in and that should get it up and running again. Saab Dastard mentioned this in an earlier post too.
The other option is that you changed the boot order for your system. You mentioned that it looks at the floppy, then the CD drive, perhaps you've told it not to look at the harddrive anymore. Check the Boot section of the BIOS to see if the harddrive is still mentioned as a boot option. It is useful to have another drive as a first boot option for use in emergencies, but have the harddrive set as second or third boot option.
Anyway, find an IDE to USB converter and copy your files first, that is the important bit. I am betting on the drive being fine though and that you'll only need to get the BIOS straightened out again.