It uploads a copy to the remote location - this is how the file-transfer protocol works, and it’s not a webMethods feature/limitation.
You need to manage the cleanup at the source, after a successful upload - you can add a local file deletion step at the end of your flow, on success (inside Try).
Alternatively, you can create a master clean-up service that will clean multiple folders, if you have a lot of file-based instances. Use a property/config type of design, instead of harcoding paths, file patterns, file age, etc. You can then create a scheduled job for this.