this saved my bacon today. My (your) hyper key mod in Karabiner Elements stopped working and KE showed a weird error. Renewing the json file didn't help, couldn't find any evidence online that anyone else was having the same problem. normal restart didn't help, but passing through a safe boot cycle did!

thank you, thank you, thank you!!!!

If you don’t know Onyx by Titanium software check it out; I believe you can delete various caches like fonts.