The decree did its work and was then left standing. Spain acquired no Jewish community to apply it to, and there was for centuries no occasion to repeal it.
The reversal, when it came, came in pieces and mostly by other instruments. The constitution of 1869 conceded a limited private freedom of worship. In 1924 a decree of the Primo de Rivera government offered Spanish nationality to Sephardim abroad who could show descent and made a claim within a period, a provision that a small number used, and which some Spanish diplomats invoked to protect Sephardic Jews during the Second World War. Religious liberty was recognised in law in 1967 and constitutionally in 1978. In 1992, five hundred years after the decree, the king attended a service at the Madrid synagogue.
The most concrete act is recent. Ley 12/2015 opened Spanish nationality to Sephardic Jews of Spanish origin who could evidence descent and a connection to Spain, without requiring residence or the renunciation of another nationality, and the preamble frames it explicitly as a redress of the 1492 expulsion. Tens of thousands of applications were made before the window closed.
What the atlas cannot state is the formal act of revocation. That the decree was revoked in the twentieth century is widely repeated, and no repealing instrument has been catalogued here. The repeal status is recorded as unknown and the open question is filed with it.