I feel like I've seen stories about this sort of thing happening a few times at least; almost invariably the newly [re]discovered animal is very similar to another species that was already known to be alive, so while still a significant discovery it lacks some punch. In this case the presumed-extinct animal is quite similar to C. electilis, which was known to be around in the modern era but apparently is poorly documented (the article says living specimens of C. electilis are undocumented so they could only compare the shells.) These are the only two known living members of the genus and both are rare, so it seems like a fairly significant discovery to me. Not really a case of "animals previously thought to be one species are now reclassified as two", like many other species discoveries seem to be.
I think situations like the Coelacanth, where the rediscovered animal is unlike any other already known to be alive, are quite rare. Although even in that case, the Coelacanth was a revelation to science but probably not the fishermen that caught it.
I recently came across this Nova documentary on the discovery of a living Coelacanth.
I think you're right, living Coelacanth's were well known to locals as they commonly turned up in the catches of fishermen, but completely amazed scientists.
I think situations like the Coelacanth, where the rediscovered animal is unlike any other already known to be alive, are quite rare. Although even in that case, the Coelacanth was a revelation to science but probably not the fishermen that caught it.