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The Library of Congress has the Lincoln Papers. Some of the collection has been digitized and are available online. You can search "West Virginia" by Keyword. The following link will take you to the collection. Abraham Lincoln Papers at the Library of Congress If the Proclamation that you are looking for is not online you can contact LOC archivist via the contact information provided on the website.
In addition, West Virginia Archives has an online exhibit about West Virginia statehood and has a copy of the Proclamation issued by Lincoln on the 20th of April, 1863: http://www.wvculture.org/history/statehood/documents/stateproc.jpg http://www.wvculture.org/history/statehood/documents/stateproc.jpg
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According to Abraham Lincoln’s 100th Presidential Proclamation, “Whereas by the act of Congress approved the 31st day of December last the State of West Virginia was declared to be one of the United States of America, and was admitted into the Union on an equal footing with the original States in all respects whatever, upon the condition that certain changes should be duly made in the proposed constitution for that State; and Whereas proof of a compliance with that condition, as required by the second section of the act aforesaid has been submitted to me:
Now, therefore, be it known that I, Abraham Lincoln, President of the United States, do hereby, in pursuance of the act of Congress aforesaid, declare and proclaim that the said act shall take effect and be in force from and after sixty days from the date hereof.
In witness whereof I have hereunto set my hand and caused the seal of the United States to be affixed.
Done at the city of Washington, this 20th day of April, A. D. 1863, and of the Independence of the United States the eighty-seventh.”
Signed Presidential proclamations are in Record Group 11, General Records of the United States Government, A1 Entry 24 (https://catalog.archives.gov/id/299955). These records are kept at the National Archives building in Washington, DC. You can email them at: Archives1reference@nara.gov to get more information about Proclamation 100.
You might also be interested in the 1870 court case that affirmed the constitutionality of West Virginia’s admission to the Union. Records of that Supreme Court case, Virginia v. West Virginia, should be available in Record Group 267, Records of the Supreme Court, which are also located at the National Archives building in Washington, DC.