Except Demak, which was founded by a Majapahit noble who married a Majapahit princess, was the state to finally destroy Majapahit. Not a foreigner. Furthermore, there is no evidence of any sort of rupture between Majapahit and Islamic Java. The same types of books were read, the same sort of culture was enjoyed, the same sort of government was employed. It was just the religion that changed (the law was still based on the Manusmrti, popular culture in Hinduism and local animism).
Borobudur was already abandoned during Majapahit.
The city of Majapahit was not forgotten and some Muslim Javanese wanted to move the capital back there to restore Java’s glory. Javanese Kings used to wear the Majapahit crown until it disappeared during one of the wars against the Dutch.
There are still Hindu Javanese around the hills in East Java.
Also, Javanese Hinduism wasn’t exactly a religion in the same vein as Christianity or Islam were. It’s a different case from the Middle East.
The two are totally incomparable.