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This is because the PID changes and the PID in the run.pid file is created by start.sh... when re-started after auto-update start.sh is not utilized, therefore run.pid isn't updated.
After an auto-update the run.pid file has the old PID in it.
Before auto update:
qortal$ cat run.pid
936
After auto update:
qortal$ ps -ef | grep java
qortal 15685 1 38 Oct10 ? 07:53:50 /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Djava.net.preferIPv4Stack=false -jar qortal.jar
qortal$ cat run.pid
936
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