Hello,
I'm using msi method to silent install skype and regedit to disable autoupdates:
start /wait msiexec /i "%~dp0%SkypeSetup.msi%" /qn
And disable update with regedit:
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Skype\Phone]
"DisableVersionCheck"=dword:00000001
You can implement the regedit command on first script.
Best regards