I had a different but similar problem when adding in a new host drive for the 64bit 7 with the same on a smaller now second drive plus setting up a dual boot with the 32bit 7 which went on last to a 3rd drive. The 32bit installer added the new drive's 64bit installation there in as a boot option but totally ignored the second drive's install there!
How to make a triple boot by unintended consequences? When going to install a Linux distro by chance on a usb flash drive the Windows mbr was trashed by Grub!
Ironically to get the mbr repaired I used the 64bit dvd's startup repair there first in inadvertently added the second drive's installation in as a new boot option. When the new drive's 64bit still wouldn't start up the 32bit dvd was then used with the startup repair and commands at the prompt to follow.
Surprize to see all 3 installations in the BCD store later!
Later the default OS was simply set in the advanced system settings>Startup and Recovery section. That saw the totally separate original stand alone install on the second drive added in showing these tools do work.
The EacyBCD program is a tool you use when mixing older versions with 7 there and could have been used for seeing the second drive's installation added in at the time. The irony was simply seeing how the repair tools worked out.