In Notepad++, there's a way to assign your custom shortcuts by going to
Run -> Modify Shortcut/Delete Command...

This brings up the Shortcut Mapper

I set up my custom shortcuts on Computer 1 I then installed Notepad++ with the same install settings and plugins on
Computer 2

I then created a zip archive of my Notepad++ folder in Program Files on Computer 1
I overwrote the Notepad++ folder in Program Files on Computer 2 with this archive

My custom shortcuts did not come across.
I thought that the shortcuts were saved in
C:\Program Files\Notepad++\shortcuts.xml

I compared
C:\Program Files\Notepad++\shortcuts.xml
from Computer 1 with the same file on Computer 2 and the
two files are identical.

Why then are the shortcuts not coming across to Computer 2?

Computer 1 is Windows XP
Computer 2 is Windows Server 2008 R2