myDir = os.listdir(r"S:SharedSanta Rosa")
for x in myDir:
  ...

for x in myDir:
    os.rename(x, x.replace('__', ''))

dirName = r"S:SharedSanta Rosa"
myDir = os.listdir(dirName)
for x in myDir:
    oldName = os.path.join(dirName, x)
    newName = os.path.join(dirName, x.replace('__', ''))
    os.rename(oldName, newName)

>>> from glob import glob
>>> import os
>>> for fn in glob("tmp/__*.pdf"):
...     print(fn)
...     os.rename(fn, fn.replace("__", ""))
...
tmp/__aaa.pdf
tmp/__bbb.pdf

os.rename(os.path.join(r"S:SharedSanta Rosa", x), os.path.join(r"S:SharedSanta Rosa", x.replace("__", ""))

dirPath = r"S:SharedSanta Rosa"
myDir = os.listdir(dirPath)
for x in myDir:
   x = os.path.join(myDir, x)
   os.rename(x, x.replace('__', ''))