If discovering which package was deleted it's enouth you can take a look at "prov_schedule.exe.log" under \program files\LANDesk\ManagementSuite\log
launch your provisioning and the log will tell you the missing package.
If you want to see who deleted the package you need to follow Sebastien post, but AFAIK it will work only if someone deletes the package from the console, it will not log the deletion if someone delete the files from disk
