Python EOFError after using os.execl to restart the script

I have a script that does the following;

• Checks if a temp.txt file is present in the working directory.
  • If present the temp.txt file and update.pyd file is removed.
• Checks whether an update.pyd module is present in the working directory.
  • If present it imports and runs it.
  • The update process creates a temp.txt file in the working directory.
  • After the update the script is restarted using os.execl(sys.executable, sys.executable, *sys.argv)

But I keep getting an error when os.execl(sys.executable, sys.executable, *sys.argv) is called:

Traceback (most recent call last):
  File "<string>", line 73, in execInThread
  File "<string>", line 44, in __call__
  File "C:\Program Files (x86)\PyScripter\Lib\rpyc.zip\rpyc\core\netref.py", line 196, in __call__
  File "C:\Program Files (x86)\PyScripter\Lib\rpyc.zip\rpyc\core\netref.py", line 71, in syncreq
  File "C:\Program Files (x86)\PyScripter\Lib\rpyc.zip\rpyc\core\protocol.py", line 431, in sync_request
  File "C:\Program Files (x86)\PyScripter\Lib\rpyc.zip\rpyc\core\protocol.py", line 379, in serve
  File "C:\Program Files (x86)\PyScripter\Lib\rpyc.zip\rpyc\core\protocol.py", line 337, in _recv
  File "C:\Program Files (x86)\PyScripter\Lib\rpyc.zip\rpyc\core\channel.py", line 50, in recv
  File "C:\Program Files (x86)\PyScripter\Lib\rpyc.zip\rpyc\core\stream.py", line 166, in read
EOFError: [WinError 10054] An existing connection was forcibly closed by the remote host

I have another process in the same script that does something similar, and restarts using os.execl(sys.executable, sys.executable, *sys.argv), but restarts cleanly.

Could someone tell me why this is happening. What "connection" is the error referring to, and how do I close it before restarting? Thanks