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John 20:27 Then he said to Thomas, “Put your finger here; see my hands. Reach out your hand and put it into my side. Stop doubting and believe.”
From what I understood Jesus was so horrifically abused that he was barely recognizable. I picture Jesus on the cross with tendrils of flesh hanging off of His back. Eyes swollen shut. Covered head to toe with blood and barely able to speak from swelling about His jaw and mouth. Did everything heal except the marks from His hands and side?
From John 20: "Though the doors were locked, Jesus came and stood among them", so Jesus seems to be an apparition, more spirit than flesh. Could it be that Thomas was instructed to put his fingers through Jesus' body because it was a resurrected "spiritual" body (the "pneuma" that Paul writes about in 1 Cor 15)?
In John, we do not read that Thomas put his fingers in Jesus' wounds. Rather, Thomas himself states that "Unless I see the nail marks in his hands and put my finger where the nails were, and put my hand into his side, I will not believe it.". "A week later...the doors were locked, Jesus came and stood among them", so Jesus did not break down the door, or pick the lock, right? He just appeared without using any doors or windows, or else wouldn't John admit that he entered through a window or something? Of course, we can't rule out a sneaky entrance from this reading, but we may agree that "though the doors were locked" was John's was to say that the room was secured from intruders.
John Chapter 20 does not tell us that Jesus appeared with any visible wounds. "Put you finger here; see my hands. Reach out your hand and put it into my side." Imagine this scene with an unmarred, un-wounded Jesus, and it still holds up. The only person who mentions Jesus' wounds at all is Thomas, and that was a full week earlier than the event! Perhaps Jesus did not show Thomas a wounded hand; rather, he told Thomas to put his fingers through Jesus' post-resurrection "pneuma" body, which enters locked rooms with no need of any material portal. A corporeal Jesus with wounded hands would have had difficulty operating an unlocked door handle, much less entering a secured room.
Jesus did not necessarily fulfill Thomas' "unless I see the nail marks" precedent. John 20 does not indicate that Jesus had any visible wounds when he told Thomas to put his finger into his side. Neither does it confirm that Thomas actually touched Jesus' hands or side, just that Jesus told him to. Those are easy dots to connect, but careful reading reveals that Jesus showed Thomas what Jesus chose to show Thomas, not what Thomas blabbed about a week earlier.
My sense is that the reaction of Thomas is not the best place to raise the question of Jesus somehow looking different in the post-resurrection appearances. Thomas had, after all, the testimony of the other ten disciples (or possibly a larger group if "disciples" is not limited to the remnant of the Twelve), and there is the clear expectation that he should not have doubted.
Other Johannine examples
There are other incidents, though. (1) In this same chapter the 'delayed reaction' recognition of Mary Magdelene in John 20:15-16 is recounted, especially:
15b NIV ... Thinking he was the gardener, she said, “Sir, if you have carried him away, tell me where you have put him, ...”
(Emphasis added.)
(2) Similarly, the prior visit of Jesus to the disciples (without Thomas) in John 20:20 depicts a positive reaction, with the implication that this comes only after signs of affirming identity:
20 After he said this, he showed them his hands and side. The disciples were overjoyed when they saw the Lord. [ἐχάρησαν οὖν οἱ μαθηταὶ ἰδόντες τὸν κύριον]
The little particle οὖν = oun can signal result ("therefore") or simply consequence ("then/when") and also suggests a "delayed reaction" in the appearance of Jesus to the disciples in Thomas's absence.
(3) A third possible example comes in John 21:4-7 when in the grey light of dawn Jesus gives instructions about fishing, and there again seems to be a delay in recognition:
7 Then [οὖν] the disciple whom Jesus loved said to Peter, “It is the Lord!” As soon as Simon Peter heard him say, “It is the Lord,” he wrapped his outer garment around him....
Here, however, the narrative setting of dawn light and distance might be enough reason to obscure the identity of the one calling from the shore.
Other Gospel parallels?
As an earlier answer notes, there might be a temptation to liken these incidents in John to the Emmaus road encounter of Cleopas and friend with Jesus, post-resurrection. There, however, it seems a different dynamic is at work to explain their lack of recognition (Luke 24:16):
16 but they were kept from recognizing him.
with the NIV here quite mild in representing ἐκρατοῦντο τοῦ μὴ ἐπιγνῶναι αὐτόν = "constrained not to recognize him". In the synoptics, perhaps a more closely related incident to those in John is the doubting noted in Matthew 28:17 (on which see an earlier Q&A, and other related ones linked there).
Beyond the Gospels
It remains, of course, speculative to link the Johannine incidents of failure to recognize the post-resurrection Jesus with the result of the physical abuse he suffered in the course of his execution. There is also Paul's teaching on the resurrection body in 1 Corinthians 15:35-49 (+ cf. Philippians 3:21) which implies that resurrection bodies have a different character than mortal bodies, especially vv. 42-44a:
42 So will it be with the resurrection of the dead. The body that is sown is perishable, it is raised imperishable; 43 it is sown in dishonor, it is raised in glory; it is sown in weakness, it is raised in power; 44 it is sown a natural body, it is raised a spiritual body. ...
Summary
In the final analysis, then, one cannot be sure that Jesus' post-resurrection "recognizability" is entirely down to the ravages experienced in the passion, as the wider NT witness suggests that the resurrection body has a distinct character from the mortal body in any case.
Likely he was completely disfigured as a result of the beating. Isaiah 52:14 prophesied: "Just as there were many who were appalled at him--his appearance was so disfigured beyond that of any man and his form marred beyond human likeness" (NIV). However, I don't think he arose disfigured. If there's evidence in the text of that, then it's beyond me. I think Thomas' need to actually touch him was more indicative of Thomas' spiritual personality, which is shown in other places, such as in John 11:16 when Thomas says "Let us also go, that we may die with him." In this bit I almost imagine Thomas like Eyeore the donkey! Don't get me wrong; I've been like Thomas many times. Remember also that the disciples on the road to Emmaus also did not recognize Jesus until their eyes were opened because of the Scriptures. Again, perhaps recognizing the risen Christ has more to do with one's spiritual eyes and less with how he actually looked.
