mstdn.jp probably needs database maintenance.
Since there are some abnormalities in the deletion process etc., it will be necessary to at least re-index. There may be duplicate data, etc., in which case you may need a maintenance command that was recently merged into master.
It's a time-consuming process, but it's a huge database, so you need to devise how to execute it.
Since it will be a surgical operation, it will be necessary to clone at least mstdn.jp and perform a dry run.
I'm not familiar with mastodon.cloud, but you may have similar issues. When Kibo Soft took over from the previous operator, there is a flow that started from the repair work of such a database.
Fortunately, the source code is almost unmodified vanilla, but it's not up to date yet. In addition, there is a problem that you can not log in related to notification, and there is a history of disabling it because it could not be solved.
The cause must be clarified and eliminated.
On the positive side, I think there is a natural attempt to integrate Sujitech's services that enable encrypted communication on existing platforms such as Facebook and Twitter into Mastodon.
I think there are other ambitious attempts that have not been clarified.
This is an irresponsible imagination, but if you become a good partner here, you may be involved in a project to reimplement SNS itself and play an important role.
There must be a fun job waiting for you as soon as you take office :-)