Minato and Hizashi created a seal to replace the Bird Cage Seal before the Kyuubi attack. Hizashi brought the seal to Sarutobi and asked for Jiraiya's services to replacing the seals on the Branch members. Hiashi empowered by Sarutobi's nearly indifferent behavior threatened to cause a civil war and kill the branch members if the seal was adminstered. The Sandaime complied.
During the time of Hinata's kidnapping Naruto sent clones to track down all branch members who were out on mission and brought them to a secret location. After the Kumo incident Naruto and Co. revealed themselves to Hizashi and told them how Danzo would threaten Neji's life if Hizaashi didn't offer his life in Hiashi's place. Neji had already been replaced with a regualr bloodclone. Naruto then gathered all the branch members in the Leaf and brought them to the secret location and redid their seal and smuggled them to Whirlpool.
See the Official Naruto Wikia.