I have a proposition of changing the behavior of queue (background) downloading/uploading.
In case of foreground usage - the prompt window with choosing the behavior (skip, replase so on) emerges when file exists.
However in case of background usage - the files are replaced by default without any questions. It's good idea to do so, as the procedure of uploading is not stopped. But probably it's better to add the configuration option (in settings) that will define what action should be done (skip, replace, continue uploading) in such a case.