Once you've selected a folder in "Browser for folder" when you are uploading or downloading files to or from your experiment, you shouldn't move the folder location on your computer. If you do happen to do this, then the files that got uploaded before the move will show in your experiment.

Uploading:

The best thing to do is to go to the experiment inbox, delete that experiment, and start over. (There's no way to delete files from an experiment once you've uploaded them.)

Downloading:

The best thing to do is to clear the files out of the folder and start the download again.