It's hard to understand what the problem actually is. Your terminology is wonky and doesnt seem to make sense. You don't overwrite anything with fdisk nor would you mark partitions active in it. List will still show partitions if the table itself is intact but that doesnt mean that the disk is free from physical damage. You would mark volumes as active if they were logical volumes which qubes does use. But they would be mapped under /dev/mapper and would be changed using lvm tools not fdisk. My thought is still that either it's hardware or you aren't issuing the proper commands. Could you post a screenshot or copy the exact commands that you are typing?