I think I know this already but not too sure on it.
Lets say I have a drive with a partition, divided into 2 drives, C:\ and D:\. If I redo the boot sector of C:\ do I loose whats on D:\ too?
You can reformat C and D will remain intact with a caveat. Any programs on D will not run until you restore their registry entries on C or reinstall the software.
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