AutoFixMaterializedView / AutoFixTempAttribute

Using PD 16.6. When updating the physical model from the repository with replacing the entire model (merge document unchecked), after the operation is ended, model still differs from one stored in the repository. Two options of the model AutoFixMaterializedView and AutoFixTempAttribute are set to true while in the repository these are set to false. Why the update process ends with the model not entirely updated with one from the repo? How to synchronize it to be 100% the same.