Changing the operating system may possibly change the interface between the OS kernel and the installed programs. If this happened, the installed program files would need to be reinstalled. I have worked with Ghost, Powerquest, DriveImage, and Phoenix ImageCast and cannot think of any of those with the option to copy only the installed program files. The copy (Ghost) programs merely do a bit-by-bit copy of the partition so they work on a much lower, physical, level than the OS. It is possible the interface between XP and MCE is the same and merely performing an upgrade would do the trick, however upgrading Windows in such a manner is not recommended since the system files of the previous OS are still mixed in with the system files of the upgraded OS. This can easily cause confusion for the NTBootLoader, which would not know which operating system to load upon booting the computer since there are entries for two systems but only a complete set of files for the new system.
For such situations, it is recommended to format the partition and perform a fresh reinstall. But there is no way I know of to then copy a set of preinstalled applications back into the OS. Specific things like memory range allocations, interrupt request lines, drivers, and other low level interface mechanisms would not be coordinated properly and I presume it would lock up the whole system.
Here is a list of partition copying programs I am aware of:
1) Unix dd command (man dd),
2) Symantec Norton Ghost, which used to be PowerQuest DriveImage and PowerQuest Recovery Environment
3) Phoenix ImageCast
4) Acronis TrueImage
5) Image for Windows