But yes, it's basically what the job comes down to - having a strategy for managing complexity in all it's forms, and this is a fine example of the sort of problem that you don't learn in college.

I've (thankfully) never deprecated code and caused serious production issues, but i've seen it happen. The best places to work expect this sort of issue, and have process in place to roll back and deal with it, like any other business continuity issue (e.g. power/network loss).

The moment you find yourself scared of changing code because you don't understand the consequences then you've basically lost the battle.