MacOS – Do I need to remove BootCamp partition before installing Mountain Lion

I know this is not a fully integrated solution, but you can use the tools available on Mac OS X and on the Mac OS install DVD/FlashDrive. You will have to restore both systems separately, but it will save you from having to reinstall everything in Windows and OS X.

Note: If your drive is phisically damaged you might end up with corrupted data or being unable to clone your partitions.

There is a thread here explaining how you can save and restore your Bootcamp partition using only Disk utility and BootCamp: http://forums.macrumors.com/showthread.php?t=997823

It goes along the lines of (parts are just copied):

• Use Disk Utility to backup your bootcamp partition to an external drive.
• You can also use Disk Utility to backup your Mac OS partition if you didn't use Time Machine.
• Install/Restore Mac OS to a new Hard Drive
• Use Bootcamp to setup your drive for windows and to allocate the new space.
• Use Disk Utility to restore your .dmg image to the new Boot Camp partition you just created. Be sure to run IMAGES --> SCAN IMAGE FOR RESTORE in Disk Utility before restoring. You may need to unmount the Boot Camp partition in Disk Utility before it begins to restore.

• Use fdisk in Terminal to mark the Boot Camp partition active. First, enter the fdisk MBR edit mode by running the following:

  $sudo fdisk -e /dev/disk0

Ignore the error "could not open MBR file /usr/standalone/i386/boot0: No such file or directory". Then, determine which partition number to mark active by running the following (in bold):

fdisk: 1> show

Your windows partition should be #3 labeled "Win95 FAT-32". Now, mark the partition active:

fdisk: 1> flag 3
Partition 3 marked active.
fdisk:*1> write
Device could not be accessed exclusively.
A reboot will be needed for changes to take effect. OK? [n] y
Writing MBR at offset 0.
fdisk: 1> exit

Now, reboot and hold the OPTION key and Windows should be listed as a bootable option."

Installing cleanly gives you the advantage that you will know if an error is due to the "as-shipped" condition of the software before you add your data and applications to the mix. The installation of a new OS is the primary time when people notice corruption of a filesystem or other hardware type errors since a machine can often keep running well with some little errors. But relinking all the kernel extensions and drivers and knowing that your accessories and applications will all take to a major new OS is a lot of change. Spending a little extra time up front can help isolate issues if you have them.

By running the migration later, you have more control over things and can also choose to hand migrate anything first that you don't trust the tools to automate.