According to a report by the Spanish internet portal "Religion Confidencial" on Sunday, the number two of the community, the nun Teresa Roca, left the convent and the schismatic community last Friday due to differences with the former abbess Laura García de Viedma (formerly Sor Isabel de la Trinidad).
Alongside the abbess, Roca was one of the plaintiffs against the archbishop and his measures.
So far there had been no contact between her and the Archbishop of Burgos, Mario Iceta. Iceta is the special papal envoy in the case of the schismatic Poor Clares.
According to him, the Church, and in particular the Archdiocese of Burgos, is "full of hope" for reconciliation with the excommunicated Poor Clares.
As the internet portal learnt, the nuns also refused to take part in a meeting with social workers. This was to further investigate the situation of the nuns.
The archdiocese was immediately informed by the social workers about the non-appearance.
In May, sisters from the convent of the Poor Clares in Belorado broke away from the Catholic Church.
After joining a schismatic bishop and later expelling him from the convent, the nuns joined the Brazilian alleged bishop Rodrigo Henrique Ribeiro da Silva at the beginning of August.
However, he too is said to have left the convent because of an uncertain future.
The schismatic and self-proclaimed bishop acted as an advisor to the nuns, but did not recognise Pope Francis as the head of the church.
The convent community originally comprised 16 sisters.
Ten of them were excommunicated by Archbishop Iceta in June; a month earlier, their religious organisation had expelled the Poor Clares.
There is now a legal dispute over the ownership of the convent.
Pope Francis has also pledged his support to the special envoy.