This should be a fairly simple adjustment. Since right-clicking and editing in WinSCP allows you to open a document for editing purposes (bypassing the default filters), when the document is saved, it should also be uploaded bypassing the default filters. Currently, it does not.
When mass-moving files, I don't want a configuration file to be overwritten, so it's on the default exceptions list. However, when right-clicking and selecting "edit", and opening it in EditPad Pro, the file opens fine, but does not re-upload after saving any adjustments that I've made.
When you put everything into something, it means everything to you.