Boot order shouldn't have changed unless you removed the BIOS battery or something so it's not that. When you say "corrupted" or "broken", what exactly are you talking about? First off, check ALL HDD-related connections (power and SATA) to make sure they are plugged in correctly. Then, if it's a fried HDD it's possible it short-circuited the motherboard's section meant for HDD connections, although that happens rarely. Another more likely cause would be a PSU issue, which again, if it's a fried disk is possible. Describe EXACTLY what happens when you try to boot, like fans spinning, disk making sounds (or making sounds and stopping for a second only to make sound again), whether there is display of any sort (if there is BIOS will pop a message with what the issue is most of the time), etc.
That's the most useless way to troubleshoot to be honest... If the issue is the HDD reinstalling Windows will only create more problems.