update #2**** Ok so it appears that once you make any changes in retroarch and save it. It stops looking in the overlay folder. I added the following to the save cfg file and it worked as expected.

video_fullscreen_x = "1440"
video_fullscreen_x = "900"
custom_viewport_x = "550"
custom_viewport_y = "0"
custom_viewport_width = "820"
custom_viewport_height = "1079"

input_overlay = "/recalbox/share/overlays/mame/16-9/pandoras_overlay.cfg"

Giving up. I tried to install from a clean install. Same issue. I have decided to go back to 8. some games also loaded up with audio but no video.

update #2**** Ok so it appears that once you make any changes in retroarch and save it. It stops looking in the overlay folder. I added the following to the save cfg file and it worked as expected.

video_fullscreen_x = "1440"
video_fullscreen_x = "900"
custom_viewport_x = "550"
custom_viewport_y = "0"
custom_viewport_width = "820"
custom_viewport_height = "1079"

input_overlay = "/recalbox/share/overlays/mame/16-9/pandoras_overlay.cfg"

Update** updated to 9.01 still broke. to fix my issue I edited the .cfg file for the overlay and now it stays. Although this is not a fix since I still can not change anything in retroarch and save it. If I do it clears out my overlay.

I am trying to figure out if its a recroarch problem or a recalbox problem.
I did notice that when I manually select the overlay and go back and save per game settings, then exit and go back in the field is blank.

well kinda fixed. if I change anything and save the game override then its gone again. nothing shows up.

Solved. did a factory reset and now they are showing up.

so I have an x86_64 setup and had all the overlays setup and looking good.
I updated to version 9 and now no bezels show up at all. I even tried to manually add a bezel back and it still does not show up. anyone have any ideas on this one?