Well, they deleted it from somewhere. As I assumed they were using a VCS I assumed they deleted it from that. Or are they really short of disk space?
Deleting "from my codebase" doesn't imply deleting it from history or backups. Just that the code isn't present for future edits or deployments.
The way you're talking, it sounds like you never delete code from your codebase. Do you just comment it out when you change a line to something else or replace a function with a new one? Just add new files?