You can write a WinSCP extension that will pre-process the file, upload it using a separate connection and post-process it.
For an example, see "ZIP and upload" extension:
https://winscp.net/eng/docs/library_example_zip_and_upload

I would like to suggest adding an extensibility mechanism which will allow to pre-process files before they are uploaded and to do post-processing after the uploading has been successfully completed. This could be useful, for example, when one wants to invoke a script to remove comments from HTML files or to strip metadata from images by invoking the command line tool of BatchPurifier Lite. The mechanism should pass the file/folder path to the invoked script and read a new path of the modified file which has to be uploaded (as the script would create a temporary modified copy of the file). The post-processing script will typically delete the a temporary modified file.