I think the SkylineCmd.exe that you are trying to run is not in the correct folder.
How exactly are you trying to run SkylineCmd.exe? If you have remembered the absolute path to SkylineCmd.exe, then that is not going to work after you upgrade Skyline, since the newer version of Skyline gets installed in a different folder.
If you do not know what directory Skyline is installed in, then you should use SkylineRunner.exe. SkylineRunner.exe looks through the Start Menu and figures out where Skyline is installed.
SkylineCmd.exe should be used if you do know where Skyline.exe is. This is what we recommend using if you have installed the Skyline Administrator version, which usually gets installed in C:\Program Files\Skyline.
SkylineCmd.exe does not know whether belongs to regular Skyline or Skyline-Daily.
SkylineCmd.exe first tries to load Skyline-Daily.exe from the same folder that contains SkylineCmd.exe. If that fails, then SkylineCmd.exe tries to load Skyline.exe.
If SkylineCmd.exe fails to load either of those two programs, then SkylineCmd.exe gives you an error. That error message is supposed to contain both of the reasons why it was not able to load either Skyline-Daily.exe or Skyline.exe.
It looks like there is a problem with how SkylineCmd.exe displays the error information, so you are only seeing the part of the message dealing with trying to load Skyline-Daily.exe.