Hi Faeran,
Using the latest beta I chose to update and replace all media for all systems and left everything checked including everything with emumovies. It updated the metadata then started the downloads like normal. When the process finished it gave me the message saying xxxx amount of files were downloaded. I opened Bigbox and force updated the game wheels. When I opened the Arcade wheel I could see right away a bunch of games were missing on the wheel. I opened Sega Genesis and there were only 2 games on the wheel. I checked the images / clear logos folder and could again tell I was missing a bunch. I tried to update all systems again but this time i just had the clear logos checked and it updated the metadata again and said it would start the downloads but nothing ever happened. I tried this 3-4 times then rolled back to 13.24 and am in the process of downloading all media and with everything checked to make sure I'm not missing anything but am not replacing anything this time.