gistfile1.py

with open('new.txt') as f, open('orig.txt') as f2:
    def zipper(f, f2):
        for line in zip(f, f2):
            yield line
            next(f2) # skip every other f2 line
    with open('out.txt', 'w') as out:
        out.writelines(zipper(f,f2))

# then replace orig.txt with out.txt
# maybe os.remove('orig.txt'); os.rename('out.txt', 'orig.txt') ?