There's no script command to do this.
However it should be relatively simple to write a script (e.g. using PowerShell) to generate a WinSCP script with a one command for each file:
put C:\Files\XYZ\June\abc.pdf /home/abc.pdf
put C:\Files\XYZ\May\jkl.pdf /home/jkl.pdf
There are more than just 2 puts to be written though.
The goal is the have an automated solution where with a statement like this
put "C:\Files\FolderName\*" -filemask=*2014/June/*.pdf|SENT_*.pdf "/home/FileFolder"
will send all the files from C:\Files\FolderName\SubFolder\Year\Month where it has a 2014\June path in it
files from those folders will go to /home/filefolder
without the folder structures and without having to create a put for ever folder structure where there are thousands.
Currently it is making a folder structure
where I would want just
Is this not possible?