But, that episode does a retcon as Dr. Tenma ONLY got the time to make a SINGLE blueprint which was for Atom, since Skunk don't knew about the other blueprint then he could get the wrong one by accident and gave to Walpurgis even with the warning.
You saw that Atom's blueprints were stolen by a flybot left by Skunk in the episode, right?
And these are the stolen blueprints from the final episode:

Note the "engrish"^^'
Dr. Ochanomizu in one of the episodes did mention that Atom's blueprints were still withn the science ministry.
So, these blueprints would be used as basis for repairs.
However, when RYOKA (which was how she was called in the original japanese) got her blueprints destroyed, the villain said he could not put her back after being disassembled, because he destroyed these blueprints himself.
So, you can figure that using Atom's blueprints would not work for her.
But, what's the point of that scientist making robots with bombs which could kill himself?
He was all like: "I'll build robo-bombs and mass produce them!!"
Just a mistake and these robots would destroy humanity including himself O_o