Why would you rebuild if you didn’t want to upgrade? Or are you now ready to upgrade?
I think all you need to do may be to checkout discourse_docker (aka /var/discourse) to a version that uses a base image that works with 2.9.0.beta9.
You’ll need to include more of the output of your rebuild. I don’t think you’ve provided the output of the actual problem.
My guess is that the database is migrated part way and something (perhaps duplicate tags due to case mismatch) caused the database not to migrate all the say. If you do not want to upgrade to 3.1.0beta4 then you’ll need to restore to your latest backup.