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The best place to find information about the publishing history of an old work with multiple editions is in the introduction to a particular edition or in a book review of a particular edition. Sometimes there are scholarly articles about a publishing history if it is interesting. There are articles about Jefferson not wanting to publish the work and his dissatisfaction with the French translation, but I couldn't find anything about its post Civil War readership. I read the introduction to the copy of Notes  (Notes on the State of Virginia. Introd. to the Torchbook, ed. by Thomas Perkins Abernethy) that we have here at the UHD library. The intro I read says that Notes was very popular during Jefferson's lifetime. In 1853 when copies of the 1825 edition were starting to run out his son gathered up all the papers related to notes and its translations and sold them to a publisher. Notes was published again in 1853. However it doesn't say what happened to the the work until it was published again in 1894 as a complete collection of all of Jefferson's writings. Then in 1955 a definitive edition was finally released (By Thomas Jefferson, ED. William Peden University of North Carolina Press, 1955). So my advice is look at introductions and reviews of different editions. Also you might want to try to contact librarians at The Jefferson Library http://www.monticello.org/site/research-and-collections/reference-question They seem somewhat restrictive, but I looked through their FAQ and their Thomas Jefferson Encyclopedia and the info they have on their website about Notes and I was unable to answer your question. I think your question should be in their scope of answerable questions. You might also ask a librarian from the Library of Congress http://www.loc.gov/rr/askalib

I have conducted an exhaustive search for this information. There might be some easy answer that I am missing that someone could easily find. However, I hope I have guided you in the right direction.