After costly negotiations and with the help of Ludwig Pfyffer von Altishofen and the nuncios Ninguarda Feliciano and Giovanni Francesco Bonomi, a catholic mutual assistance pact was signed on 28 September 1579 in Lucerne and all parties swore to uphold the pact on 11 January 1580 in Porrentruy.

[1] After the oath in Porrentruy, he began to spread the Counter-Reformation into the territories that surrounded Basel and had some political ties to the city.

The resulting conflict between Basel and Blarer ended up before a Swiss Confederacy arbitration court and was settled in 1585 in the Baden Agreement.

In this treaty, the city provided an oath of allegiance, its influence in the Herrschaft of Erguel was restricted and the Burgrecht agreement with Bellelay Abbey was dissolved.

[1] While the Baden Agreement had helped the shattered finances of the diocese, Jakob Christoph now sought to prevent renewed debt.

With the reopening and expansion of the mines and iron forges in Courrendlin, Undervelier and Belle Fontaine (now part of Saint-Ursanne) he created new revenue sources.