It can be rather easy, when editing the raws or doing anything else there, to get a backup copy of the changed file. While many programs use different filename extensions from the original file, and as such aren't used by Dwarf Fortress, some instead change the filename itself without changing the extension (to creature_standard (copy 1).txt for instance), and those files are read, potentially leading to very buggy worlds.
As such, I would suggest that the game pops up a warning, similar to the embark warnings, if it encounters duplicate errors when you try to generate a world. This could potentially extend to a few other errors that impact generation (such as the skipping of generated creatures if you mess with the standard body materials), but those generally require more modding involvement on part of the player. You probably could choose to ignore the warning if you really wanted to see such a world.