Sys folder placed into retroarch/system/dolphin-emu makes some roms crash instantly, just saying, maybe i can help with this (So Retroarch does recognise that path despite telling you that the folder is missing). For example i was trying to run Baten Kaitos for GameCube, crash everytime. Then i deleted that folder and now it loads without problems (User folder into saves is harmless instead, and will be reacreated, if you deleted it, everytime you load a rom). And if i add Sys folder content to User folder content, CRASH happens again. So the problem is definitely something inside Sys folder, i’ll try every file inside it to isolate the problem.
EDIT: yeah ok i found out the problem in my case, it was a string inside GKB.ini (GameSettings folder) related to Baten Kaitos: CPUThread = 0
After deleting this no more crashes.
So, if some games are crashing on load, search in GameSettings folder some strings related to them.
Or simply delete GameSettings folder.
Tested on vulkan driver and Windows 7.