Well I would recommend uninstalling the agent then letting provisioning install the agent but if you must clone here is a script we used to use:
set CWD=%~d0%~p0
cls
C:
CD %CWD%
ECHO Stop LANDESK Services
net stop "LANDesk Policy Invoker" /yes
ECHO %ERRORLEVEL%
net stop CBA8 /yes
ECHO %ERRORLEVEL%
net stop ISSUSER /yes
ECHO %ERRORLEVEL%
net stop "LANDesk Targeted Multicast" /yes
ECHO %ERRORLEVEL%
ECHO Deleting LANDesk Directory
IF EXIST C:\ProgramData (
RMDIR C:\ProgramData\LANDesk /S /Q
ECHO %ERRORLEVEL%
) else (
RMDIR "C:\Documents and Settings\All Users\Application Data\LANDesk" /S /Q
ECHO %ERRORLEVEL%
)
ECHO Deleting Registry Common API for LD Agents
IF EXIST "C:\Program Files (x86)" (
ECHO Deleting Common APIs for new agents 64bit
C:\Windows\System32\Reg delete "HKLM\SOFTWARE\Intel\LANDesk\Common Api" /f
C:\Windows\System32\Reg delete "HKLM\SOFTWARE\LANDesk\Common Api" /f
C:\Windows\System32\Reg delete "HKLM\SOFTWARE\Wow6432Node\Intel\LANDesk\Common Api" /f
C:\Windows\System32\Reg delete "HKLM\SOFTWARE\Wow6432Node\LANDesk\Common Api" /f
ECHO %ERRORLEVEL%
) else (
ECHO Deleting Common APIs for new agents 32bit
C:\Windows\System32\Reg delete "HKLM\SOFTWARE\Intel\LANDesk\Common Api" /f
C:\Windows\System32\Reg delete "HKLM\SOFTWARE\LANDesk\Common Api" /f
ECHO %ERRORLEVEL%
)
EXIT /B %ERRORLEVEL%