If I check the BIOS and reset it if necessary for 1048 cyl, 16 heads, 63 spt etc, would I endanger any info on the HDD?
If the BIOS was configured to address the disk with those parameters (and it should have been, given that they are written on the disk), then no. If, for some reason, the parameters used were different then possibly, but that's highly unlikely. There may be an "Autodetect" setting in the BIOS which you can try.
If these were changed would it mean that the HDD is as it was, but the PC is looking at it "wrongly" now, so doesn't recognise anything on there?
Yes. This is one possibility for the PC not booting from the HDD. Changing the boot order or simply disabling / removing the HDD in the BIOS would have a similar effect.
If the BIOS settings are wrong and I change them, would anything overwrite to the HDD or is it just the EPROM on the Motherboard that gets changed?
As long as you don't enter incorrect drive parameters, then the data on the HDD shouldn't be affected, as you say you will just be changing settings in the BIOS on the mobo.
I'm impressed at the whopping 540MB disk size!
My first PC was a 486SX that had a 100MB disk with 4MB RAM.
SD