The paths to the media files you removed are exactly what connects the media files to the GEDCOM data. SO without them, naturally the files become “Unused”.
In all kiwitrees installations media is stored in the /data/ folder. Within that it “might” be different (but yours at kiwitrees.net isn’t). So, providing you don’t change the defaults, which are to store media in the /media/ folder (which is also true for your online site) then you don’t need to change or remove anything from the GEDCOM when you move it, or start a local copy.
So, to put it simply, you are over-thinking the issue.
Re-export your GEDCOM file. Change nothing else. Leave your local media where you have put it. Then re-import it into your local site. Everything should now work as normal.