In the future, you may need to use Auditing option (See link below). It tracks what people do on the console basically. Check if this provisioning part is one of them;
The link for auditing:
In your case, you won't be able to figure that out unfortunately. Even in the DB, you can't. But in table PROV_TEMPLATE_DEF, you can find the date when the template was last modified without knowing who.
I hope it clarified things up at least.
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
Thanks for the replies, I will enable logging and start keeping track.