I've flown turbo-prop RPT a number of times from Kupang to Sulawesi and below FL200, you'd be well out of any civilian radar coverage.
If they flew a direct route from Kupang to Manado, at below 10,000 ft, they would have been well clear of civilian secondary surveillance radar all the way until about 70 miles from Manado.
I'm actually surprised Indonesian radar picked them up at all, considering they let a B777 fly through without detection a few months ago.