Related question: For the updates, when prompted "Updated underlying kernel, OS, etc" - Why does that update point to the kernel that kills the HDMI video out? Anybody else who updates their system and chooses to updated the underlying kernel/OS is going to run into the same problem. Just wondering why nobody's changed that to point back to the last kernel that doesn't kill the video.
The OS updates are not distributed by RetroPie, but are coming straight from upstream Raspbian distribution. If you have a video initialisation issue with a certain update, most likely is because of a firmware update.
Try telling the boot loader/firmware what resolution do you need by modifying the config.txt file and tweaking the video resolution parameters - see https://www.raspberrypi.org/documentation/configuration/hdmi-config.md.
What version of the Raspbian kernel are you using ? Can you run uname -a from a terminal and post the output ?