Francisco Aparicio was one of six Franciscans assigned to unsuccessful missions founded on the San Gabriel River in the late 1740s. After the murders of Father Juan José Ganzabal and Juan José Ceballos (1752), relations between the remaining clergy and the presidio commander, Felipe de Rábago y Terán, continued to worsen. A second priest at San Gabriel had already died of natural causes; a third determinedly remained at his mission. But Father Aparicio fled to San Antonio with two other clerics, and they did not return to their missions until after the panic had subsided.
In July 1755 Aparicio joined soldiers of the presidio in requesting permission to move the failed settlements to the San Marcos River. By August 16 the two remaining missions and a presidio had been relocated without formal approval of the viceroy. On August 23, 1755, Father Aparicio and two fellow priests petitioned the new military commander, Pedro de Rábago y Terán, for reassignment among Lipan Apaches on the San Saba River. That request was denied.
Aparicio then participated in the temporary transfer of San Francisco Xavier de Horcasitas Mission to the Guadalupe River. Immediately after the deaths of fathers Alonso Giraldo de Terreros and José de Santiesteban at Santa Cruz de San Sabá Mission (March 16, 1758), Aparicio was sent there by Mariano de los Dolores y Viana. Three weeks after the destruction of the mission Aparicio asked that the site be abandoned and that further efforts be directed to the San Marcos or Guadalupe rivers. Widely experienced among diverse enemies of the Apaches, such as the Mayeyes, Yojuanes, Bidais, Orcoquizas, and Cocos, the padre raised serious doubts about further attempts to missionize the Lipans.
By October 1758 Father Aparicio had returned to San Antonio, and he was present during the interrogation of Apache chief Tacu, which centered on the advisability of founding new nations for his people. As plans progressed in San Antonio for a punitive expedition against the northern nations that had destroyed Santa Cruz de San Sabá, Francisco Aparicio supplied ten Indian auxiliaries from Nuestra Señora de la Purísima Concepción Mission.