Maybe I did the update incorrectly. One thing that confused me in the video is what folders and files to copy. At 2:26 it says to copy over "assets, autoconfig, config, states, shaders, filters, saves, overlays, retroarch.cfg, retroarch.default.cfg, retroarch-core-options.cfg". At 3:32 it says the three most important things to copy are the "config folder, retroarch.cfg, and systems folder". I copied over the assets, autoconfig, config, states, shaders, filters, saves, overlays, AND systems folders, and the retroarch.cfg, retroarch.default.cfg, retroarch-core-options.cfg files. After the update when my other games would not work I pointed the games back to the old RetroArch (1.2.2) version.
Not sure if this what you mentioned, in LaunchBox on the left side it says "Nintendo Game Boy Advance". Also, in the 'Edit Game' window under the 'Emulation' tab and the 'Edit...', the 'Emulator Name;' is "Retroarch" for all systems I use (SNES, SMS, G&W, N64, GBA).
Here is some more info if I didn't provide enough information previously. I updated everything from within RetroArch (core updater, info files, assets, etc). When I double-click on a Game Boy Advance game it will not run, however, the ‘Play Count’ note in the details increases by one without actually opening RetroArch. I tried running the games with these cores: gpSP, MednafanVBA, mGBA, VBA Next, VBA-M. Currently I am using RetroArch version 1.2.2