Techniques are provided for handling misaligned holes and writes beyond end of files during a quick reconciliation process. During quick reconciliation, a read operation is performed to read data from a first storage object and is replicated to a second storage object. If the data read from the first storage object comprises misaligned holes, then a different range of data is read from the first storage object so that aligned holes are read and replicated to the second storage object. If the read operation targets a region beyond an end of the first storage object, then the second storage object is truncated to a size of the first storage object.