Ok, stinks for me...thanks anyway...

Sorry, but we cannot support 3rd party program here.
Your existing syntax (special.exe put C:\local\out\ remote/in/ y) is not a valid "WinSCP" syntax. So it's obvious that special.exe uses a different syntax than WinSCP. So we cannot advice, how to modify the syntax for your new needs.
If you want, we can help you re-implement your functionality using WinSCP proper.

Ok, well the subject says it all.
The current bat file contains:
C:\Program Files (x86)\WinSCP\special.exe put C:\local\out\ remote/in/ y
As you can see we hit up an inherited exe to then help with the put.
I tried doing something like this:
C:\Program Files (x86)\WinSCP\special.exe put -permissions=755 C:\local\out\ remote/in/ y
which logs this: session xmlns="http://winscp.net/schema/session/1.0" name="C".
I assume the C is just referring to everything after the put & permissions.
My question is this...given the original bat file, is there a way I can add the needed permissions, with out finding and updating the original "special" exe? ( Currently we don't have access to the source...don't ask...)
Thanks for any help.