Is there a way to replace files, like a version control, or is the process to upload a new one, and manually go to the asset manager and clean up old files?
As for the “renaming files with numbers in front”, it does appear to be your plugin doing that as the filenames have wpdm in it. (Does not appear I can attach files, and since this is your plugin renaming files in asset manager, I don’t see any reason to have to upload a screnshot, I just need more info about this then).
Any info for both of these issues would be great.