I have noticed reverts whenever an edit is being made to OSD script. When you hit that "Save" button anything that you modified in "Advance Edit" gets wiped out. Im not sure if its exactly the same issue you are having but i usually disable the Edit on my scripts and only work with them in Advance Edit so they dont get reset.
Also for sysprep changes, i normally dont use the LANDesk template builder. I create my sysprep with WSIM (win7) and like you i place them in a sysprep repository and i call them during the end of the OSD process.
REMEXECXX=cmd /c copy /y \\syspreplocation\Unattend.xml c:\windows\panther
REMEXECXX=cmd /c copy /Y \\syspreplocation\sysprep.inf c:\sysprep\sysprep.inf
it makes updating sysprep files much easier then going back into the GUI
That's the thing, it appears as though someone went into the Edit on every OSD Script(have at least 30 b/c of branch offices) and then hit save to revert the changes. But only 3 people have access to the OSD responsibility.
did you install a remote console somewhere? there was a bug that reset all OSD scripts when a remote console was installed.
EDIT: - here is the article http://community.landesk.com/support/docs/DOC-22422
We had our xml and ini set to read only. The only downside to this is to remember to go in a uncheck the read only if we want to make any chances to the script.