(16:03:33) | Entity is NULL but is still in saveList - not destroyed properly? item_drop_backpack[249026199]

(16:03:33) | Entity is NULL but is still in saveList - not destroyed properly? item_drop_backpack[252729894]

(16:03:33) | Entity is NULL but is still in saveList - not destroyed properly? item_drop_backpack[246878954]

(16:03:33) | Entity is NULL but is still in saveList - not destroyed properly? item_drop_backpack[246306759]

(16:03:33) | Entity is NULL but is still in saveList - not destroyed properly? item_drop_backpack[252407753]

(16:03:33) | Entity is NULL but is still in saveList - not destroyed properly? item_drop_backpack[249847924]

(16:03:33) | Saved 159,372 ents, cache(0.33), write(0.04), disk(0.03).

(16:03:33) | Saving complete

Does anyone know how to solve this problem without deleting all data?

Yes, entities that were spawned at a previous location; to which the game had since saved, and those are simply null valued expressions the server outputs for stdout. It just states 'hey, these were spawned entities in our last save, but not now, whats going on?' 

means nothing important.