Has there ever been a case of historical documentation that was mistaken for fiction and then later reevaluated as truth?

Yes

There were a lot of Greek inventions, such as gear chains or using mirrors to start fire, which were dismissed by historians. Everyone "knew" Greeks were like Romans, so it was assumed that like Romans, Greeks despised machinery. The few fragments which survived in written documents were dismissed as later day dreams, rather than practical working inventions. When these showed up in medieval engineering books, they were assumed to be new inventions (even more so when they showed up in Da Vinci's notebooks.)

Then they started discovering things like fifty gear astrolabes to predict a calendar more exact than any ever used by Romans. Then they found things like gear trains and that you could use a mirror to set fire to a ship. That the steam engine was invented before Christ. They realized that high tech mines in France were Gaulish, not Roman.

They realized the Romans weren't the advanced civilization they'd thought they were, but a military society which had destroyed the more complex Gauls, Dacians, and Greek civilizations. That the complex machinery of greece had been abandoned for Roman entertainments. Teat the Dark Ages weren't when Rome fell, but when Rome conquered.

Actually the dragon situation is true. And there are still dragons...but they don't look like what you're thinking. But back in the day? There are bones of animals that would pass for dragon-like creatures. It's not fiction.

There are plenty of other things. Ghost, poltergeists, cryptids, etc. There are plenty of things that people believed in and saw long ago but were then interpreted as fake and then later revealed to be true.

Yes. Here are some examples.

Kraken: It is a giant, tentacled, sea monster of Norse myth that is now widely believed to be based upon actual encounters with the giant squid. The kraken legend already occurs in Medieval texts, but the giant squid did not become known to science until the 19th century.

http://www.unmuseum.org/kraken.htm

Norse discovery of America: Before the discovery of Viking artifacts at L'Anse Aux Meadows in Newfoundland back in 1960, historians disputed the veracity of the Norse sages describing their voyages to America. Some believed these sagas, but others regarded the stories as little more than fiction. Pre-Columbian European folklore abounds with mythical tales of strange islands and unknown lands in the Atlantic Ocean that are quite obviously fabulous, like "Hy Brasil" and the lands described in "The Voyage of Saint Brendan." Some scholars classed the Norse sagas describing their voyages to unknown lands to the west of Greenland alongside these fictional legends. But archaeology proved these sagas to be essentially correct.

Many examples of historical documentation that was originally mistaken for fiction (or outright lies) and later proven to be true exist in the accounts of the early explorers and travelers. For example, early European explorers in Africa received some ridicule for describing man-like beasts covered with hair. These were of course chimpanzees and gorillas.

http://listverse.com/2010/04/16/10-beasts-that-use...

Troy was thought to be fiction till an archeologist found it.

when you ask a question if something has EVER happened, most certainly the answer has to be yes.