How do you know they/ Thomas are "referring back" to Jesus talking about returning to Jerusalem?
I didn't say returning back to Jerusalem; I said returning back to Judea. Both Jerusalem and Bethany are in Judea. In fact, they are less than 2 miles apart.
https://en.wikipedia.org/wiki/Bethany
They'd just come from Jerusalem in Judea, where people had tried to kill Jesus. Now Jesus is proposing going back to Judea to Bethany, only two miles from Jerusalem. This is why Thomas is concerned about dying.
And here's a thought. Thomas who is said to be among the witnesses to this so called “dead” Lazarus miracle doubted the Christ himself had also raised from the dead, Why!? Hadn’t he witnessed Jesus himself raise a dead man!? Hadn’t the Christ continuously told his followers that he would rise from the dead? One has to ask why he doubted his masters resurrection after what he and the disciples been told and what he himself had witnessed?
Indeed, we should ask that question! Thomas had seen what Jesus could do; it was completely irrational for him to doubt Jesus. And yet, that is a common pattern. The Israelites saw God send plagues to Egypt and part the Red Sea, and yet they doubted again and again on the way to Canaan until God said they weren't to enter it until that generation had died off. Gideon saw an angel, yet still asked for a sign - and then asked for another sign! The people who were at the feeding of the 5,000 and personally saw Jesus do a miracle asked Him for a sign shortly afterward, as if He hadn't just done that. The disciples do it multiple times. They see the feeding of the 5,000, and the feeding of the 4,000, and yet are still concerned when they forget to bring bread. Jesus even calls them out on this:
Mark 8
14 Now the disciples had forgotten to take bread, neither had they in the ship with them more than one loaf.
15 And he charged them, saying, Take heed, beware of the leaven of the Pharisees, and of the leaven of Herod.
16 And they reasoned among themselves, saying, It is because we have no bread.
17 And when Jesus knew it, he saith unto them, Why reason ye, because ye have no bread? perceive ye not yet, neither understand? have ye your heart yet hardened?
18 Having eyes, see ye not? and having ears, hear ye not? and do ye not remember?
19 When I brake the five loaves among five thousand, how many baskets full of fragments took ye up? They say unto him, Twelve.
20 And when the seven among four thousand, how many baskets full of fragments took ye up? And they said, Seven.
21 And he said unto them, How is it that ye do not understand?
I have seen people I know who have seen God's work in their lives doubt Him in similar circumstances. I have seen myself do the same. It is irrational, and it is illogical, but it is a very human thing to do.
The prodigal so was not “dead” was he? But his father said he was “dead” and he also said that he was “alive” again after being “dead”.
Then we notice that as quick as one can be raised from the “dead” one can it seems, also return to being “dead” when we look at the story of Ananias, and Sapphira his wife, Acts 5:1-11. Taken literally here we have two people just dropping down “dead” and getting buried, for no other reason than they hadn’t handed over money to god (the cause). And, to be cast out at such a crucial time must have been a terrifying punishment considering they believed that the “kingdom of god” was just around the corner. If they wasn't then we’d have to ask why all of those present were? Acts 5:11
You are right that the prodigal wasn't physically dead, but there are some important differences between the prodigal and Ananias and Sapphira and Lazarus. In the prodigal's case, the details mention show that he was physically alive. He ran toward and embraced his father; those are actions done by a living person. I mentioned in my earlier comment how the physical details in the Lazarus story show that the story is talking about someone who was actually, physically dead. And in the Ananias and Sapphira story, the details also support a physical death.
Acts 5
5 And Ananias hearing these words fell down, and gave up the ghost: and great fear came on all them that heard these things.
6 And the young men arose, wound him up, and carried him out, and buried him.
Ananias fell down, was wrapped up, and carried out. These details are consistent with someone who died physically. The details are similar for Sapphira.
More broadly, spiritual death is indeed a thing, but it does not follow from the existence of spiritual death as a concept that every mention of death in early Christian writings is therefore talking about spiritual death and not physical death. Physical death is still a real thing that Christians in all ages have to talk about. Indeed, it would be wildly implausible for there to be a religion that had nothing to say about physical death at all. Now for a thought experiment: put yourself in the shoes of an early Christian writer who wants to write about someone who died. How do you communicate to your readers that you're talking about physical death? You could, of course, explicitly write "This is physical death, not spiritual death" every time you want to do that, but that is very cumbersome. Short of explicitly spelling it out every single time, what is sufficient to communicate that you're talking about physical death? If talking about someone who got sick, died, was wrapped in burial garments with a cloth over the face, was buried in a grave some distance from the house, was mourned by Jews, and stank because he had been dead four days doesn't communicate that you're talking about physical death, what in the world would communicate that? That's not just rhetorical (although it is rhetorical too), that's a serious question. If you were an early Christian writer, how would you communicate that you're talking about physical death without having to explicitly say it every single time?
As a final point, there are a bunch of details in the Lazarus story that contradict the idea that this is a spiritual death.
1. 8 His disciples say unto him, Master, the Jews of late sought to stone thee; and goest thou thither again?
If this is about spiritual death, why are the disciples concerned about stoning?
2. 16 Then said Thomas, which is called Didymus, unto his fellowdisciples, Let us also go, that we may die with him.
If spiritual death is being outside of Jesus' movement and this is talking about spiritual death, how can the disciples die "with him"? Jesus can't very well not be in Jesus' movement.
3. The Jews in the passage:
31 The Jews then which were with her in the house, and comforted her, when they saw Mary, that she rose up hastily and went out, followed her, saying, She goeth unto the grave to weep there.
36 Then said the Jews, Behold how he loved him!
37 And some of them said, Could not this man, which opened the eyes of the blind, have caused that even this man should not have died?
45 Then many of the Jews which came to Mary, and had seen the things which Jesus did, believed on him.
Why are people who didn't previously believe in Jesus mourning that Lazarus had "died", i.e. was no longer one of Jesus' followers?
4. 47 Then gathered the chief priests and the Pharisees a council, and said, What do we? for this man doeth many miracles.
48 If we let him thus alone, all men will believe on him: and the Romans shall come and take away both our place and nation.
Why would the chief priests and Pharisees think this was a miracle? Lazarus leaving and then rejoining Jesus' movement isn't remotely miraculous and wouldn't cause anyone to believe on him.