I don't know who to give credit for this concept, but I'm a fan of "tombstoning" functions that are being removed. You basically replace (or prepend) the body of the function with a call to a method that logs the timestamp, calling function, etc.

Here's an example in PHP from a quick google:

https://github.com/scheb/tombstone

I once had to lead a large refactor of a project written in an foreign dynamically typed language and tombstoning was a necessity for how large and poorly designed the projet was.