I was able to reproduce the problem. It only happens if the file set to be executed after the update has not changed in the update. Either that, or if the whole folder has not changed. (I tested with only a single file).
Are the files E:\Wedigo.net\1.0.0\npm.exe and E:\Wedigo.net\1.0.1\npm.exe identical?
Also, are the folders E:\Wedigo.net\1.0.0 and E:\Wedigo.net\1.0.1 identical?
I'm guessing that's a bug in WYUpdate...
Here's a workaround for now.
Include a new bat file in your project, and execute npm.exe through that bat file.
Then for each of the versions 1.0.0 and 1.0.1, modify the bat file - even if the npm.exe files are identical, as long as the bat files are different (just add a few spaces or modify something in them), wyUpdate seems to execute them.