Meaning it will upload the changed files as new ones, not change the ones on the remote server, right?
The problem is that I don't know where all those redundant files are. When DW finds all the links to change, can you get a log or a list of all those files, so you know where they all are?
What I understood was that you wanted to rename a folder. Dreamweaver will handle the local change of links for you. You then upload the changed files with the modified links as well as the files that have been placed in a new folder. All you need to do now is to removed the old folder from the remote.
Alternatively, you could change the name of the folder on the remote which will save you having to upload the files to the new folder.