BU / restore of one NON OS partition changed BCD, Boot Mgr

Using Ghost 15 SP1 on Vista x86 (for this problem).

 

Most recent, I simply made BU of the APPLICATIONS partition (D:\) from an old disk (no longer booting disk - w/ Vista), & restored it to new disk.
NOTHING else was included in the BU image - JUST D: off old disk. The "new" disk has been running / booting w/ Vista just fine for couple wks.  Were no longer any options given in Vista Boot Mgr for other OSs, at startup - fixed that.  Booted correctly into Vista that I copied weeks ago, to new disk.

AFAIK, nothing in this BU / restore operation should touch the OS, BCD, MBR, Boot Manager - but it DID. Ghost 15 restore of D: to a partition on NEW disk worked (the new partition already existed)...BUT ,  ALSO completely messed up BCD & Boot Mgr. Had to use trial boot disk of BootIt bare metal, to fix.

 

Restore of BU of D (Applications) off old disk, to D on new disk, changed BCD settings (like under Menu:  Path & System root) from what were correct, functioning values for ONE booting OS, so that NO Windows would boot AND reinserted older Menu - Vista entries (that also had some property errors).

 

1)   In the restore setup options:

* chose Verify recovery point before restore

* did NOT choose Check for file system errors

* did NOT choose Set drive Active (for booting OS)

* did NOT choose Restore original disk signature (because wasn't restoring to orig source disk)

 

As soon as "Successful" restore finished, rebooted - got typical "Windows has encountered errors...please insert orig disk."  I used the Vista recovery CD - did it's thing, but still didn't boot.  Started BootIt boot disk & saw the mess.

 

Why would a BU & restore of non OS, non booting partition mess up BCD, boot mgr or do anything w/ OS partition? 

How can I prevent this from ever happening again? 

 

Could have just copied the data over for this type partition.  Never dreamed it would touch the OS, but now I'll BU BCD, bootmgr (not w/ Ghost or other imaging prgm!) & save trouble next time Ghost or others go psycho.

 

BTW, are there any freeware prgms similar to BootIt that have boot disks, if needed?  I may not use software like BootIt for another 5 - 10 yrs.  There's a free GUI version of BCD Edit, called Visual BCD Editor http://boyans.my3gb.com/.

EasyBCD only works if have a booting Win OS.  Other than those, not sure.

 

Thanks.