It would be mostly impossible to "fix" this by only overwriting files, since the world files store 32x32 chunks each. You will need a special program for that to pick just the single chunk.
As for the location, the formula is simple, filename is "r.<floor(ChunkX / 32)>.<floor(ChunkZ / 32)>.mca", where the "floor" function rounds the number towards negative infinity.
As for the location, the formula is simple, filename is "r.<floor(ChunkX / 32)>.<floor(ChunkZ / 32)>.mca", where the "floor" function rounds the number towards negative infinity.