hum,

it's about going to the directory of a file if you dump a file over the icon.

see in env_for_icons.bat

rem default is as before: Winpython ..\Notebooks
set WINPYWORKDIR1=%WINPYWORKDIR%

rem if we have a file or directory in %1 parameter, we use that directory 
if not "%~1"=="" (
   if exist "%~1" (
      if exist "%~1\" (
         rem echo it is a directory %~1
	     set WINPYWORKDIR1=%~1
	  ) else (
	  rem echo  it is a file %~1, so we take the directory %~dp1
	  set WINPYWORKDIR1=%~dp1
	  )
   )
) else (
rem if it it launched from another directory , we keep it that one echo %CD%
if not "%CD%\"=="%~dp0" set  WINPYWORKDIR1=%CD%
)

if it doesn't fit you, you can keep using "%WINPYWORKDIR%"

I use E:\Github\WPy64-3940\Jupyter Notebook.exe , and change settings/winpython.ini , but failed launching from other directory, is it not the right way to work in other directory?
#WINPYWORKDIR = %HOMEDRIVE%%HOMEPATH%\Documents\WinPython%WINPYVER%\Notebooks
WINPYWORKDIR = E:\Github\Repositories

I think the problem is that the WINPYWORKDIR1 is assigned in env_for_icons.bat before evaluating the content of winpython.ini.
I moved the block FOR /F "delims=" %%i IN ... in env_for_icons.bat before the assignement and it works for me.

was the problem solved ?