Ask user for "Overwrite/Resume/Skip".
Another disturbing question, that would be useful only for minority of users. Sorry :-(
OK. You are the boss. But with respect,
at the moment, WinSCP 3.1 asks for file overwrite confirmation,
and the choises are: Yes/No/Abort/Yes to all/No to all. If resume is permitted by the protocol, adding Resume to that list is not big problem to user, IMHO. If I remember correctly, if resume is permitted, there is another window asking for resume, and to get there, you have to press Yes on the Overwrite-confirmation-window.
ncftp is well-known and behaves this way: asking for resume/append/overwrite if the file alredy exists. wget's resume also assumes that if the existing file and the file to be transferred have same name, resume happens. But in those cases one cannot see from the file(name) if the transfer is complete or not, in WinSCP's case you can see that. But still the triggering of resume-action is different, which in itself is not a bad thing, but confusing for many.