I had the same problem as today, starting from 4.5.6 to 5.4. I managed to get around the problem by returning to 4.5.6 and then moving back the old way, that is, ignoring the new update instructions.
The environment was Windows10 / Postgresql4.3
Further research showed that I skipped a step in the new instructions, namely deleting the data / es directory.
I migrated several times, and if I run the default default database to check and update plugins, but forgot to delete the / es data directory before switching to postgresql, then the quality profiles will get null rules, but if I follow the instructions correctly, the profiles will correctly transferred.
Please check your procedures against http://docs.sonarqube.org/display/SONAR/Upgrading
Hope this helps
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