I just tried updating to the latest version through itch, and it completely borked my RA installation irreparably. Most of (if not all) of the internal files (such as shaders, controller profiles, etc) are now all in a single folder. I've had to uninstall and revert back to 1.10.3 (fortunately that one still seems to be fine).

Ditto, I use Itch to keep my RetroArch installation and cores up-to-date, and this latest release has pretty much destroyed my installation. The RetroArch installation doesn't extract properly, and the cores don't extract at all (just a 7z folder sitting in the install location).