Complex sentence: The Dutch also will not attempt to interfere or wage war against Johor, in effect the agreement limited Dutch influence in the Malay Peninsula in contrast to the other part of the archipelago which would become the Dutch East Indies.
Split into simpler sentences: The Dutch also would not attempt to interfere or wage war against Johor. In effect, the agreement served to limit Dutch influence on the Malay Peninsula in contrast to the islands of the archipelago which would become the Dutch East Indies.