Comments - MariaDB removes all users on restart
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FOUND THE ANSWER.
Really strange if you ask me. When changing the config files I had set the variables like so :
WAIT_TIMEOUT = 6200 INTERACTIVE_TIMEOUT = 6200 INNODB_LOCK_WAIT_TIMEOUT = 120
I believe it caused a syntax error in the config file. I changed the variables to lower case and it worked fine. Maybe it got to the config file and failed and then didn't continue with the setup after restart. Shout out to Ben for the help!
Next time check if mysqld is running. If it is not, check the error log.