Methods and apparatus, including computer program products, implementing a technique for repairing links in a file. The file can contain one or more links, each link referring to a target file. For one or more of the links, a file identifier such as a file name, file number, or file address is stored. Alternatively, for one or more of the links, target information is stored that identifies an old target and a new target for the link. The links can be repaired based on the stored information. The stored information can be used to identify changes to the links that occurred while the file containing the link was inaccessible to the system, for example, due to the file being locked by a user.