My computer refuses to boot windows but the circumstance is odd

basically i have a 1tb hdd as my primary hard drive and everything worked swimmingly i had the harddrive partitioned for organization (two 500gb partitons) and then i added a laptop drive for an extra bit of storage, it was an old oem drive and had a 10gb system partition and a 800mb hidden partition, everything worked ok i just ignored the extra partitions, then i pulled the laptop drive out of my system and used dBan on it to nuke it as i had to use it in another system, now my system refuses to boot, i get the message reboot and select proper boot device or insert media into selected boot device, i put the windows install disk into my system and tried a system repair but it refused to see my hard drive and wouldnt detect it, the hard drive is seen in the bios however, i have temporarilly connected a 40gb hdd with windows installed on it and disconnected the 1tb drive, i have never used raid, i have never changed any bios settings except from overclocking, please tell me theres a way to fix this