Both premises of the OP is wrong, first that the prologue might be separate and second that the Valentinians only used the prologue.
Origen's commentary on John goes into detail about how the prominent Valentinian Heracleon interpreted the Samaritan Woman story in John, and even notes that in verse 4:18 Heracleon reads six (ἕξ) husbands instead of five (πέντε), thus interpreting it as all material evil. A Valentinian fragment from Clement Stromata references John 8:44. The Gospel of Phillip, which many think is Valentinian, references John 8:32-36. Hippolutus (Refutation of all Heresies 6.30.1) says the Valentinians used John 10:8 to support their claim all the prophets, therefore, and the Law spoke by means of the Demiurge, "fools who knew nothing."
Then I got some coffee
my brain kicked in, remembering Heracleon wrote a entire commentary on the Gospel of John, which is where Origen got his quotes. It has in fact been suggested Origen wrote his commentary on John in reaction to the Valentinian commentary. See
http://gnosis.org/library/fragh.htm for full list of
So the second premise is refuted decisively; the Valentinians made extensive use of John beyond the prologue. Stephen Huller's interpretation of Irenaeus on this point is (as with many), to say the least, faulty.
On to problems with the second premise of the OP that the prologue was a separate document originally than the Gospel of John. There is a wide range of opinion on the composition of the 4th Gospel, but there is consistency with the rest of the Gospel in both theology and theme. I am in the five layer composition camp, but I see the first two layers as fused in the first published version. DCH points to two parallels from the 2nd "narrator" layer that is on top of the episodic layer. But he only hints at the consistency of the prologue to the rest of the Gospel. I will just mention a couple more.
Before that I'll digress into the uniqueness of the logos identified as Christ himself in verse 1:1 (and 1:14), which sets the prologue apart (I had often wondered, on the idea the prologue was separate, if λόγος had replaced φῶς or φωτός, as Jesus refers to his word as a doctrine, but himself as the light in the rest of the Gospel). But even this is actually a story about the origins of Jesus, and verse 1:14 makes that clear where the pre-existing Christ (becomes flesh in "grace and truth." The prologue, I argue, is meant to counter Matthew's protoevangelium birth account (Matthew 1:18ff). Aligning the arrival of Christ with Colossians 1:15-17, and Phillipeans 2:6-7 in Marcionite form (reading ἀνθρώπου for ἀνθρώπων γενόμενος with
p46 syrJ cop Origen), and the reputed position of Apelles (Hippolytus Refutation 7.27). Note to Joe Wallack, this is one of many points where John is responding to elements in Matthew not found in Mark (no such the other way); and this continues elsewhere refuting his protoevangelium, specifically Matthew 2:1-6 by John 1:41-42 ("Jews" = "Judaizer Christians" ask how John's Jesus can be Christ since he is supposed to be from Bethlehem, not Galilee, per Luke 4:31 in the Marcionite account) - another element not found in Mark.
The consistency of the theology with the rest of the Gospel can be seen in verse 1:17 with the formula juxtaposing Moses with the Law (i.e., the books of Moses) against Christ who brings "grace and truth." This happens in 5:45, 47 (I'm not certain about 4:36 being in the original version of John), 6:32-33, 7:19, 22-23, 9:28-29 also perhaps 3:14 (as an allegory) in the discussion with Nicodemus. This is also seem in Jesus' denigration of the Law and thus Moses as not his in verses 8:17, 9:34, 15:25. Those who support Jesus (crowd = assembly) are said to not know the Law in 7:49, and when the assembly (crwod, this time "Jewish Christains") challenges Jesus as contradicting what is predicted in the Law in verse 12:34. There is no theological split with the rest of the Gospel. In fact it fits the narrator's themes.
The same can be said of the light and life in the prologue (verses 1:4-5) reflected in Gospel verses such as 3:19, 8:12, 9:6, 11:9-10, 12:35-36. The material about John the Baptist as a witness contained is a summary before the fact has already been covered (the often before the fact narrator commentary of events is one of the reason I think the episodic material was first, then a 2nd author placed a narrative layer, including the prologue). Note on John the Baptist, in the prologue John is said to be sent by the God of Jesus (not the Law giver; separation of Law giver from Demiurge is a major theological break between John and the Marcionite type theology), consistent with the presentation in John, and in opposition to the Elijah come again theology in Matthew.
The case is not strong for the prologue existing independent of the Gospel. It is far too close thematically and specifically to the theology found in the Gospel. So the case is not made for the first part of the OP.
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note to DCHindley on his listing of Greek and English of the prologue verse 1:11. The English translation is rather loose, with subjective renderings:
εἰς τὰ ἴδια ἦλθεν -> "came among his own"
// where did "house" come from? οἰκία simply isn't there in the Greek, nor is τόπον αὐτῆς
καὶ οἱ ἴδιοι αὐτὸν οὐ παρέλαβον --> "and those who were his own did not receive him"
// own "people" is suggestive; λαόν ἴδιοι is not what is written
The readings with those two "implied" words seem to me to be theologically driven by the translator, perhaps even unaware. Taken together I get the view he is reading in Jesus as Jewish and coming into his home, but being rejected by the Jews. But there are other readings possible. One, which Giuseppe would jump on, is that Christ came among the his own celestial born beings (demons, spirits, etc) but they didn't receive him, in fact opposed him -- before this he dwelt with his father. I am not advocating this reading, just pointing out how the translator by inserting two words not in the Greek. You should have bracketed [house] and [people] as implied words like you did [Son] in verse 1:14 for example from μονογενοῦς .
(IMO the articles like "the" you didn't need to bracket, as they are required by English, and you can capitalize if you want to emphasis uniqueness)
“’That was excellently observed’, say I, when I read a passage in an author, where his opinion agrees with mine. When we differ, there I pronounce him to be mistaken.” - Jonathan Swift