It seems like one of the mods we used to use has an effect that is supposed to delete players after 365 days of inactivity. However, a few users on the minetest forums have been reporting that it has been deleting players much quicker than that.
I think this may have effected some users on the server and I am just posting this as a notice in case some people were affected. Server cleaner is no longer in use in the code/game/server as of a month ago. This should not be a problem any longer.