If you try to boot a moved clone of 2K/XP without editing the boot.ini file then it would appear like you were indeed booting into the clone when in fact you were actually booting into the parent that the boot.ini was still pointing to. The same happens with a clone of Vista if the BCD file is not altered correctly. It will look like you have successfully booted the clone when in fact it will be the parent install of Vista that will be booted. Look in Disk Management and you will see the real System and Boot partitions. Hiding the parent when booting the clone does not help as the parent will still be targeted. You will then get an Autochk Program not Found or a blue screen error part way into the attempted boot of the hidden Vista. If the Disk Management utility shows the system and boot partitions as expected, but the drive letter as seen from inside the new clone is not the same as it is inside the parent, then you have cross-linked OSes. Move some icons on the desktop and then boot into the parent, if the changes are there as well then you know you have a problem.
If you make a complete sector-by-sector clone of a drive containing Vista then you will duplicate the disk signature and the partition offset and so you will not have to modify the BCD to get Vista booting, because it will already contain the correct information. Be aware however that you cannot have two hard drives on the same computer with identical disk signatures. If you boot any WinNT operating system when there are two drives with the same signature then one of the signatures will be automatically changed. If you do clone a Vista drive in this way and need both drives connected at the same time then generalizing the BCD before cloning, or re-specializing or generalizing the BCD on the affected drive, will fix the problem. This has always been an issue when cloning entire hard drives containing WinNT, but before Vista a signature change could in many cases not cause an issue and so may have went unnoticed.
If you do have a problem with a clone assigning itself the wrong drive letter then you will still be able to boot Vista by clicking through various dll errors and eventually get to a limited desktop, or in some cases just to a completely blank light blue screen. In previous WinNT recovering the OS from this situation could be difficult, but in Vista it is relatively easy and can be done from the loaded desktop. All you have to do is change the drive letter to what it needs to be. Once you reach the limited desktop press Ctrl+Shift+Esc or Ctrl+Alt+Del to open Task Manager and then click 'new task...' and run compmgmt.msc and once the console opens select Disk Management from the list of utilities and then determine what drive letter has been assigned to your clone. Then 'new task ...' again and this time run regedit and navigate to the key described in the screenshot below. Right click on the \DosDevices\ entry that has the letter currently assigned to the clone and choose 'rename' and change the letter to the one the parent sees itself as when you are booted into it. If your clone's registry already has that letter assigned to another DosDevices entry you will need to change that one first to free up the required letter. You can make it anything for now as you can change it again later in Disk Management.
If you don't get a limited desktop but only the blank blue screen then you probably won't be able to open Disk Management, but regedit should still work. You can make an educated guess to which entry is the clone and change its letter and try rebooting. Repeat if necessary with all the entries until you get the right one. Or you could just delete all entries and let Windows completely rebuild the list on reboot. This may do the job, or just take you back to where you started. Completely clearing the drive letter list is a useful trick in XP based operating systems to cure drive letter problems, (for 2K OSes there are other factors that can make it hazardous). It does have its risks however and should not be attempted lightly for anything other than boot drive primary partitions. For second or higher hard drives or logical partitions, or if you are using the MS bootmanager, you should use with caution or know what you are doing. For Vista OSes that are already having problems then you have little to loose and should still be able to recovered with the procedures described here.
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