Some habitats are clearly more susceptible to the preservation of fossils.If those specific habitats are not occupied by a particular kind of creature, it may not be preserved in the fossil record even though it is still alive and well in some other habitat.
Generally, species that use a wide range of resources or tolerate a variety of abiotic conditions can establish more populations in more places than comparable species with relatively narrow niches (Brown, 1995; Cook and Quinn, 1995).
Then they suddenly disappear from the fossil record some 80 million years ago only to reappear alive an well swimming around in oceans today.
Clearly, some types of coelacanths lived in habitats that did not lend themselves to fossilization while others did.
The scientific method can only disprove theories or increase the power of previous predictions that have yet to be disproved, but it can never absolutely prove anything to be absolutely true.
Therefore, the best thing to do in science is to continually question and test previous hypothesis and theories to see if they continue to hold up under scrutiny.