Just had the same problem.
In my case, I found that Grafana could not write into the /var/lib/grafana/plugins directory, as the ownership (after adding in other plugins before the upgrade) was not grafana:grafana.
Changed permissions of the folder accordingly, performed an install of the Elasticsearch plugin (via the UI), and restarted the grafana-server service (existing Elastic datasources were not found until this occurred).
I fixed the issue by simply mounting an empty directory to /usr/share/grafana/data/plugins-bundled/elasticsearch, which means that the started container no longer has a bundled elasticsearch plugin. Then I added elasticsearch to the plugins to be installed, and I have the newest version installed without Grafana every trying to uninstall an old version.
The solution is implemented in the grafana helm chart via option shadowBundledPlugins
by mounting additional emptyDir.
This worked for me with Grafana 13.0.3.
When will this be included in the grafana operator CRDs?