Я думаю, что лучшее решение будет примерно таким:
Ваша обычная программа:
...
# ... part that downloaded newest files and put it into the "newest" folder
from subprocess import Popen
Popen("/home/code/reloader.py", shell=True) # start reloader
exit("exit for updating all files")
Сценарий обновления: (например, home / code / reloader.py)
from shutil import copy2, rmtree
from sys import exit
# maybie you could do this automatic:
copy2("/home/code/newest/file1.py", "/home/code/") # copy file
copy2("/home/code/newest/file2.py", "/home/code/")
copy2("/home/code/newest/file3.py", "/home/code/")
...
rmtree('/home/code/newest') # will delete the folder itself
Popen("/home/code/program.py", shell=True) # go back to your program
exit("exit to restart the true program")
Надеюсь, это поможет вам.