I remember having TimeoutStopSec in my cardano related systemd configuration set to a low amount of seconds. That made the OS kill the process everytime it was restarted as the process could not finish shutdown in that timeframe. End result was a long startup as it needed to fix the db.
Check if that applies to your config too. Maybe you can explicitly set that value to something like 60 seconds. The default should be 90 seconds but I’m not sure if that gets overridden somewhere.