From the early 18th century Marathas consistently attacked Jinjira. In 1733, Maratha forces captured much of the surrounding area of Murud-Janjira fort. Through they did not take Janjira fort but a favorable treaty gave the them indirect control over virtually all of the Janjira's land. When British come to the region, constant raid of Marathas in sidi's land is stopped. And maybe for protection from the Maratha or fearing of losing with British the nawab of Janjira agreed to administered as part of the Bombay Presidency as a princely state.
This is quite unclear. Many princely state was resistant to joining India. But, no resistance from Janjira state was seen in integration with India. May be the join willingly or they join for diplomatic pressure from Indian politician.