Were the deleted "files" actually folders?
if so, create a text file called "LeaveMeHere.txt" that contains a comment as to why you are using it, and place a copy in every folder in the archive job. Then edit your Global Exclude list with a path of "\\*\*" (any server, and folder) with the file name LeaveMeHere.txt and specify /SUBDIR
This should preserve the folder structure even if you Archive/Delete all the actual data.