Freeform Lite update on Craft 2 deleted tables
But on my remote server it deleted two thirds of the tables in the db.


That sounds like some update failure happened, Craft tried to roll-back and restore the database from its pre-update attempt database backup because https://docs.craftcms.com/v2/config-settings.html#restoreDbOnUpdateFailure is set to true, then plot twist another failure happened before it could restored and left the database in an inconsistent state.

There are tons of reasons an update might fail to go through, and nearly as many for why a restore would fail, but a good place to start would be your craft/storage/runtime/logs files as well as your web server's log files.