Rest assured that if you upload new files to Moodle, by dragging-and-dropping or selecting via the browser's file upload dialog box, they overwrite the old ones - usually you get a dialog box to confirm the overwriting.
There were a few issues with the HotPot module not always being aware that a file had been updated and continuing to display the old file content. However, hopefully those issues are fixed in the latest version of the module. Please update when you have a chance.
regards
Gordon