Some embodiments provide a method for a network controller that manages multiple managed forwarding elements (MFEs) that implement multiple logical networks. The method stores (i) a first data structure including an entry for each logical entity in a desired state of the multiple logical networks and (ii) a second data structure including an entry for each logical entity referred to by an update for at least one MFE. Upon receiving updates specifying modifications to the logical entities, the method adds separate updates to separate queues for the MFEs that require the update. The separate updates reference the logical entity entries in the second data structure. When the second data structure reaches a threshold size in comparison to the first data structure, the method compacts the updates in at least one of the queues so that each queue has no more than one update referencing a particular logical entity entry.