Again, the brothers from the court of Sobotište before the approaching Betlén troops resorted to safety below the castle Branč. In a fire in the castle below in October 1623 they burned things worth thousands of gold and lost 31 brothers. A few days later, the Ottoman soldiers arrived in Sobotište in the service of the rebels, who dragged away two 14-year-old girls and took three horses. From April to June 1624, thousands of Polish soldiers operated on the Moravian-Slovak border. Brothers, like other residents, have abandoned their dwellings. On the night of 12. 6. 1624 the soldiers attacked their camp below Branč. Relatively quiet period lasted until 1645, when Juraj Rákoci with his troops twice camped near Sobotište. In both cases, it cost the brothers a lot of bread, wine and beer. After the departure of the soldiers, the plague spread to which many people died at the end of 1645. Similarly, in June 1661, the brothers had to feed German soldiers who moved across the mountains. According to estimates, only military protection cost at least 150 gold.
Two years later, during the siege of the fort of Nové Zámky, part of the Ottoman troops undertook robbery attacks, during which in early September 1663 invaded Záhorie. In the early morning of September 4, 1663, the town of Sobotište and the brotherly court were invaded. They captured 24 people and killed 8. The brothers lost all grain and flour. They captured 122 people from all the brothers’ courts in Slovakia. Only 3 have been liberated. In addition to soldiers, the fraternal court was also destroyed by several floods and fires. The oldest flood captured in the chronicles affected the anabaptists in 1630. One old brother died. Six years later the whole court burned down. The misery was so great that the elders proposed to leave Sobotište and split among the other fraternal courts in smaller groups. They notified their decision to all compossessorate of the manor who asked them to stay. They gave them help and exempted them from all charges and work for two years. With the help of brothers from other courts they had the whole court almost rebuilt for the winter of 1636.
After 60 years of the 17th century , nearly annual military spending, along with the devastating floods of 1672, 1675 and 1678, were the main causes of the transition from joint to private farming. The total disintegration of community management in Sobotište occurred in the first half of the 90s of the 17th century.