At the Paris church, Saint Denis Basilique, where France has buried it's royal dead for centuries, a large crypt reportedly contains the remains of Marie Antoinette and Louis XVI (d.1793) along with those of several others including the last Louis, the XVIII, who reigned from 1814-1824.
http://www.mike-reed.com/images/Famous%20Dead%20People/Louis_16_King_of_France_-_Paris_France_1.jpg
Louis XVIII also built La chapelle Expiatore (1816) as a memorial to those two, (described as "over his brother's grave" on some pages) and the 3000 or so others who died in the Revolution.
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The fun part is they are probably in both places or neither. To wit:
La Chappelle Expiatore This small chapel honors Marie-Antoinette and her husband King Louis XVI,
whose bodies were unceremoniously dumped into lime pits here, after their beheading (along with 3000 other headless Revolution victims, including Charlotte Corday, who assassinated Marat, and Madame DuBarry, mistress of Louis XV). Whatever your thoughts on Marie or religion, this feels like a sacred place. There are statues of Marie and Louis, a beautiful dome, and an underground chapel and crypt. The park outside (Square Louis XVI) is a peaceful slice of green in an otherwise busy section of Paris.
Louis XVIII had Louis XVI and Marie-Antoinette's remains transfered to the royal tomb in St-Denis in 1815, 22 years after the guillotine had ended their lives. At his request this memorial chapel was built (1816-1826) to honor the
first resting place of his brother and his sister-in-law.
My emphasis above.
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My answer to you, dov, is that graves and gravesites are often symbolic. I believe that is the case here unless someone can show that French science had progressed in 1815 to the point of today's DNA testing. Finding the right (headless, limed) bodies would have been impossible at the time, so some remains were removed and moved, crypts erected and dedicated, and the French went on with lives. There is the possibility I suppose, that even in the chaos of the Revolution certain parties kept track of whose body/head went into the pit and where it was last seen, but I haven't found anything to indicate that that happened.
Joe