Based on the reported condition of the skeletons, I doubt there is any recoverable DNA from those newly discovered bones in Indonesia. Still, the Negritos have been in the Philippines for a long time, perhaps over 20,000 years. That suggests an overlap in timeline between the two peoples. Negritos are the aboriginal people of the Philippines. They're also quite short. It's conceivable that there is some relationship between them and the Indonesian people. A natural disaster that wiped out a population in Indonesia probably wouldn't seriously impact people living in the PI.

On a side note, it'd be interesting to do a DNA analysis comparing the Negritos with Australian aboriginees. There has been a lot of intermarriage between the Negritos and other Filipinos, so the comparison might be tough. However, mitocondrial DNA analysis might reveal some interesting information.