In addition to other treacherous acts, Boone had to complain of the friars tampering with his soldiers and slaves, and encouraging them to desert.

In order to put an end to the evil, he banished all the Portuguese friars, and installed in their place an Italian bishop and some Italian Carmelite friars.

This was held by the Goa authorities to be an infringement of the rights of the King of Portugal.

In retaliation, all Roman Catholics in Bombay were forbidden to recognize the authority of the Italian bishop and friars, and the Portuguese General of the North was ordered to prohibit all intercourse with Bombay, and to inflict the severest penalties on all persons attempting to go there or to leave it.
"Those who are captured shall be whipped and put in the galleys for five years, and, if of noble birth, they shall pay the sum of one thousand xeraphims in lieu of working in the galleys, and shall be transported for five years to the fortress of Diu."[1] It seemed as if Boone was to have a Portuguese war added to his other troubles.

Fortunately, more moderate counsels prevailed, and, in September, a conciliatory letter was written to Boone by the Viceroy, announcing his approaching departure.