A new paper in the journal Nature makes the case that "Hobbit" remains on the island of Flores are 110,000 to 60,000 and that the associated stone tools are not younger than 50,000 years BP. Thus, hobbits and modern humans may have co-existed no longer than Neanderthals did in any one place, rather than co-existing for 30,000+ years as suggested by previously estimated dates.
This actually makes a great deal of sense. In every other case where modern humans co-existed with another hominin species, or even with another highly diverged and technological disparate population, the "less advanced" population quickly went extinct leaving only minor genetic traces in the surviving population and perhaps some tiny isolated relict populations.
Hobbits (a.k.a. Homo Florensis) are certainly the most plausible candidates to have admixed with early Papuans and Australians who arrived in Flores ca. 50,000 years ago to give them high levels of Denisovan admixture (although they may have been genetic close relations of a taller and larger Denisovan species from the mainland that experience island dwarfism on Flores and this size disparity may have made love rather than war a more palatable option upon encountering them since they wouldn't have been as threatening to modern humans).
But, there is no genetic evidence to suggest a sustained period of admixture as recently as 12,000 to 18,000 years ago, with 32,000-38,000 years of co-existence, when the previous dates suggested that Hobbits went extinct on Flores. We would also expect significant change in the hobbit phenotype over that time period as hybrid individuals came into being for sustained periods of time. If that was the case, modern humans on Flores would have much higher proportions of archaic admixture than Australian Aborigines or Papuans who swiftly moved on from Flores to more distant destinations on what was apparently a one way voyage. Yet, this is not what we observe.
This does leave up in the air the speculative linguistic evidence that Hobbit language learners may have influenced the language of Flores (making it simpler), and the plausibility of the oldest oral histories regarding people who might have been Hobbits, each of which seem more doubtful at a time depth of 50,000 years than they do at a time depth of as little as 12,000 years.
One possibility that could partially reconcile the two lines of evidence is that a minority of Hobbits who survived encounters with modern humans relocated to less accessible locales and were more wary of modern humans after negative initial encounters with them, but still persisted in small, isolated relict populations whose remains have not been located yet that gave rise to the oral histories at least.