@mitu I had no luck with Skyscraper, it did not find any of the missing PC Engine CD games the normal way.
How do I scrape by MD5 using the --queryoption?
UPDATE: Ok, so three weeks later, being stubborn and refusing to give up, I finally managed to download the missing video snaps for those five PC Engine CD games!
What I did, was to place those five PC Engine CD games into /home/pi/RetroPie/roms/pcengine, then I scraped with skyscraper and it managed to find the video snaps for those games. I set the video path to each game from /home/pi/.emulationstation/downloaded_media/pcengine/videos/game name.mp4.
I thought I would just update my last post incase anyone else is having the same problems that I had.