is there a way to add an option to have it sync changes to the files, but prompt when a file is created/deleted?
possibly have a setting in the options page on either adding the missing file (as it is now) or prompting to either add or remove?
Just to be sure, if I understand what you want: When WinSCP detects a change, it should display some confirmation before actually performing the synchronization, right? Something like synchronization checklist for full synchronization?
This is not that easy to do conveniently. Because, if you refuse to add/remove certain file once, the directories will stay unsynchronized. So with every future change in the same directory, you will be prompted with the unsynchronized file again and again. It is even worse that Windows report changes time to time, that makes no difference to you, but WinSCP cannot know that and you will be prompted with the file, even if you actually do not change anything.