<<...now is my question in these: What will be happen now.?>>
That's easy, so I'll try it
The fact that each hard drive has a boot partition and a different O/S...is meaningless, in a sense.
If both O/Ses are Windows and the system is relying on Windows boot files
to determine which O/S to boot into...it will go by which those files. Windows will look at the drive designated as the boot drive in the BIOS (first), then the boot files on said drive.
If each O/S is installed individually, with no intention of a dual-boot...the boot files will reflect only one option. Windows will only try to boot into the hard drive which is the option selected in the BIOS. The fact that there are two drives...makes no difference, since only one is selected as the first option in the BIOS. I suppose that if that drive becomes defunct, then the other drive would be selected...or if the other drive is selected in the BIOS, the system would try to boot into it. But the BIOS options point the way initially for the system.
If the two O/Ses were intended to be used as a dual-boot, either by modifying the Windows boot files or the use of a 3d-party tool, (such as EasyBCD or GRUB)...then the system user will have the option of determining which O/S to boot into. The Windows files will reflect a dual-boot and the screen will show both O/Ses as a choice, with one of the two designated as the default option. The user can change this option at any time.
Some persons don't understand this about the drive letters...any system that Windows boots into will always be considered C: by Windows, once the user is in Windows. The other O/S automatically should be seen as the next available drive letter...unless the user has been fiddling with drive letters.
I have a dual-boot on this system...XP on one partition, Win 7 on next partition, same drive. When I boot into either O/S...it becomes C: and the other becomes E (optical drive takes D:). There can only be one C: active/open at any one time...and whichever I boot into...is it.
Sooo...to answer your question...it all depends on the boot options which a given user has chosen to use.
I could have 5 hard drives with a different O/S installed on each...that would present no problem at all to Windows or whichever bootloader I chose to use. There would be no confusion because the boot files tell the system which ones are bootable...and which one to boot into.