No, this is not supported.

But it should not be difficult to script this using WinSCP .NET assembly from a PowerShell script (or other language).

I am looking at synchronizing local files with remote ones. My difficulty is that I want to put the files into a subdirectory at the remote site. That is:

For any newer file found in directory 'alpha' locally put the newer file into the remote directory 'alpha/input'.

I want to use the /input subdirectory at the far end so that I can delete any other files in there and not touch the user's files in his main (remote) alpha directory.

This goes for all of the many local directories. (The local directories are all of the one depth.)

That is, any newer files in 'beta' directory should go to remote 'beta/input'

In short, would something like this work:
synchronize remote -delete d:\*\* e:*/input/*