Jhieminga
It is actually possible to corrupt a HDD by entering the wrong value for cylinders when setting CHS parameters (enter a value in excess of the maximum and stand well back), but unlikely to have been done here.
Good call on the boot order - might be that straightforward.
Also wondering if any rejigging of the IDE cable / jumpers was done, so that Cable Select no longer recognizes the disk because it's on the wrong connector - if the OP was trying to add a 2nd HDD. Or if a 2nd HDD was added without configuring the jumpers correctly (master / slave / CS) - that's a good way to prevent any drives being detected.
Slightly puzzled by the "it said it couldn't find Windows, only DOS came up" statement - that sounds like the disk IS being seen for DOS to boot, but the Windows installation isn't starting correctly. There's something in the back of my mind though that is nagging me about old PCs booting into ROM BIOS (that looks like a DOS prompt) if no boot medium is found. It's nearly 30 years since I last saw that, so forgive the memory lapse!