I've done some tests recently and it seems the video_threaded = true setting is causing the black video in RetroArch.
If you're willing to give it a try, modify the setting in /opt/retropie/configs/all/retroarch.cfg or through the Advanced configuration editor and
put back gl as video driver
disable the threaded_video setting.
After the configuration is modified, you can test again any libretro ROMs/Games - no restart/reboot required.
I emailed them. They told me it may got bent. Looked at it the card got bent, don't even know how it got bent. Sigh. Ohh well i gotta get a new card now sigh.
It managed to fix its self. Trying to delete the file another way the whole system crashed and led me to an abort screen. When I rebooted the system everything worked fine.
@BuZz Thanks for the tip. I'll post this over there to see if anything positive can come of it. At least replacing a single-board computer is MUCH cheaper than a PC.