I see some evidence that makes me suspect that this issue (or a very similar issue) was thought to have already been fixed, but:
When I try to run “Applications ➤ Task Toolkit ➤ Restore Tasks ➤ Restore RetroArch Overrides”, it says Error: No bind map entry for ‘/opt/muos/share/info/config’, and it indeed doesn’t get rid of my overrides. This is on a TrimUI Brick Hammer (so only one SD card), which had been flashed with Jacaranda and then updated to Funky Jacaranda with the update archive. My Anbernic RG-35XX H—on which I am also only using one SD card—exhibits the same issue.