There's no easy way to do this with WinSCP (nor any other tool I know).

It's easy to recursively iterate the tree finding files matching a mask using WinSCP .NET assembly from PowerShell script.
See for example https://winscp.net/eng/docs/library_example_recursive_search_text

But WinSCP .NET assembly does not support changing permissions, only scripting interface does.
But you can use the .NET assembly to search for the files and make it generate chmod scripting command for each matching file. And then execute the script.

Hello,
I want to change the permission (chmod) of some files with the same file extension,
which are not in the same directory.
More than 50 files somewhere in 100 directories.

I have no permission to unix console, but to FTP.

How can I do this?