The true answer regarding any question about whether a given passage was in the Autograph™ or not is that we really don't know. The fact that a given passage, verse, word or phrase is in the oldest manuscript on hand doesn't guarantee that the same passage, verse, word or phrase was in even older manuscripts that are lost. By the same token, the fact that a given item might be in a later manuscript but not earlier ones doesn't guarantee that the item wasn't in some still older lost manuscript. We might infer some things about the presence or absence of an item in various manuscripts, but we can't usually (if ever) prove those things.
What we do know about the pericope of the adulteress (John 7:53-8:11) is summarized in Metzger's Textual Commentary on the Greek New Testament (2nd ed.): "The evidence for the non-Johannine origin of the pericope of the adulteress is overwhelming" (in laymen's terms, "We don't believe it was in the original"). It is missing from early manuscripts and from the important Sinaiticus (א) and Vaticanus (B) codices, both of which date to the early to mid 4th centuries (they are the oldest complete Bibles we have). John Chrysostom (c 349-407), probably the premier Greek commentator on John in antiquity, doesn't address the passage in his commentary. Nor does the latter Byzantine commentator, Theophylact of Ohrid (1055-1107). It is thought to be a largely western addition to the text, although Jerome (347-420) wrote:
In the Gospel, according to John, there is found in many of both the Greek as well as the Latin copies, the story of the adulteress who was accused before the Lord.1
Augustine actually speculated that the text had been removed by some in order not to somehow encourage adultery, as the account portrays the Lord forgiving it.2
Metzger's detailed commentary reads:
It is absent from such early and diverse manuscripts as 𝔓66, 75 א B L N T W X Y Δ Θ Ψ 0141 0211 22 33 124 157 209 788 828 1230 1241 1242 1253 2193 al. Codices A and C are defective in this part of John, but it is highly probable that neither contained the pericope, for careful measurement discloses that there would not have been space enough on the missing leaves to include the section along with the rest of the text. In the East the passage is absent from the oldest form of the Syriac version (syrc, s and the best manuscripts of syrp), as well as from the Sahidic and the sub-Achmimic versions and the older Bohairic manuscripts. Some Armenian manuscripts and the Old Georgian version omit it. In the West the passage is absent from the Gothic version and from several Old Latin manuscripts (ita, l*, q). No Greek Church Father prior to Euthymius Zigabenus (twelfth century) comments on the passage, and Euthymius declares that the accurate copies of the Gospel do not contain it.
When one adds to this impressive and diversified list of external evidence the consideration that the style and vocabulary of the pericope differ noticeably from the rest of the Fourth Gospel (see any critical commentary), and that it interrupts the sequence of 7:52 and 8:12 ff., the case against its being of Johannine authorship appears to be conclusive.
"At the same time", the Commentary argues, "the account has all the earmarks of historical veracity."
It is obviously a piece of oral tradition which circulated in certain parts of the Western church and which was subsequently incorporated into various manuscripts at various places. Most copyists apparently thought that it would interrupt John’s narrative least if it were inserted after 7:52 (D E (F) G H K M U Γ Π 28 700 892 al). Others placed it after 7:36 (ms. 225) or after 7:44 (several Georgian mss)4 or after 21:25 (1 565 1076 1570 1582 armmss) or after Lk 21:38 (f 13). Significantly enough, in many of the witnesses that contain the passage it is marked with asterisks or obeli, indicating that, though the scribes included the account, they were aware that it lacked satisfactory credentials.
Based on all of the above, the Nestle-Aland committee couldn't bring itself to completely eliminate the passage from the Critical Text, but they decided to place square brackets around it. Some English versions based on the Critical Text (e.g. RSV) place the passage in a footnote, but I am not aware of any modern versions that eliminate it altogether. The passage is in the Textus Receptus, Majority Text, and the later Byzantine Patriarchal Text, so Bible versions based on those texts include the passage; as do all versions based on the Vulgate (e.g. Douay-Rheims).
1. Against the Pelagians, II.17
2. On Adulterous Marriages, II.VII.6