I threw the question of filling and recutting into the mix as a possibility, but without any proof either way.
It could be partly rubbed down and recut. The evidence from some coins dating to the civil war shows underlying detail that can be identified as being from a particular (different) die. This only predating your coin by a few years suggests that it was standard practice at the time. Pre-Civil War, I have a type 4 halfcrown with a star mark overlying an anchor. Anchor is unknown on a type 4. Similarly there was a type 3 halfcrown went through Lockdales in the past year or so with an underlying Portcullis, used on type 2 coins of that denomination.
Engraving the dies on the end of a piece of hand-held bar for hammered coins is more flexible than dies used for mechanical presses where the surfaces need to be more consistently parallel given the mechanical alignment of the press. A seriously undulating die face in the latter case would produce inferior coins.