Provided are a computer program product, system, and method for fixing anomalies in a preserved data structure used to generate a temporary data structure during system initialization. A preserved data structure in persistent storage is used to build a temporary data structure in a memory of the computing system during initialization of the computing system. The temporary data structure represents computational resources in the computing system and is rebuilt from the preserved data structure during the initialization. The preserved data structure and the temporary data structure are processed to determine whether the preserved data structure includes at least one anomaly that would result in rebuilding the temporary data structure with an error. Information on the preserved data structure and the temporary data structure having the anomaly are processed to determine modifications to correct the preserved data structure. The determined modifications are processed to correct the preserved data structure.