Use raw transfer setting
https://winscp.net/eng/docs/rawtransfersettings#excludeemptydirectories
Like this:
ExcludeEmptyDirectories
:
https://winscp.net/eng/docs/rawtransfersettings#excludeemptydirectories
Like this:
synchronize remote "D:\Camera" "/share/Videos" -rawtransfersettings ExcludeEmptyDirectories=1