If you'd ever need to downgrade, you have to drop the "new" closure table and either manually restore its original structure, or let midPoint do it (if hibernateHbm2ddl=update). In either case, however, the table will be empty, and there is no automatic procedure that would fill it in. One possible solution then is to export all organizations and reimport them. The closure will be recomputed during that process.
TODO some notes on configuring closure-related actions at startup (checking, rebuilding)
TODO about manual check/recomputation of the closure (About->xxx menu item).