These two things are related to each other. Your server ID changed because your database URL changed.
And your projects list was “initialized” (re-set to empty, right?) because you pointed SonarQube at an empty database.
I advise double-checking the $SONARQUBE-HOME/conf/sonar.properties of your 8.9 instance and copy/pasting the database-related setting from it into your 9.9 config. Hopefully a restart of your 9.9 instance will then get it pointed at your old/existing database, pre-populated with all your old projects.