His governorship was deeply unpopular with the inhabitants of Asunción, and an investigation by judge José de Antequera y Castro of the Real Audiencia of Charcas concluded that Reyes had abused his office, and he was deposed.
Reyes also taxed important members of the Paraguayan elite to fund the construction of defensive fortifications.
Annoyed at this, Antequera sent men to Corrientes, where they kidnapped Reyes and brought him back to Asunción, where he was kept nearly in solitary confinement for more than a year.
Reyes was only released after Antequera was deposed as governor, but not wishing to incite the Paraguayans to revolt, he was quietly told by the Spanish government to move somewhere else.
Little is known as to what happened to Reyes afterward; he moved to Lima and in 1733, the Viceroy, the Marquis of Castelfuerte, issued an official document absolving him of all the accusations made against him during the Revolt of the Comuneros and by Antequera.
However, his son Don Carlos de los Reyes Balmaseda did return to Asunción, and became a member of its cabildo in 1740.