Destruction of secondary disk by start-up scandisk

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Archived from groups: microsoft.public,microsoft.public.win2000.general (More info?)

If you are a user of Windows in two languages, especially one in one
byte system(such as English) and the other in two bytes system(such as
Japanese), you must have wondered whether you can use a partition
manage/format utility software for both languages. In my experience, the
partition manager which is written for English comes up with "invalid
format" when used for Japanese Windows.
More serious problem is when I set up two drives (one with English
Windows as Primary(C:) and the other with Japanese Windows as
Secondary(D:) in order to use certain files stored in D, The computer
starts with checking file systems(Scandisk) of both drives and finds the
D drive "damaged" and attempts to "fix" it unnecessarily. The result is
destruction of the boot sector (MBR?) of D making it unbootable or
inaccessible. (When the disk is used next time as primary, BIOS
recognizes its presence but next is the "Blue Screen" after Windows'
logo and installation progress bar.)

Can someone tell me how I can restore thus damaged boot system?
Is there any way to prevent this scandisking of secondary drive?