Ok so when the game first came out I remember a Train Tunnel just beneath dead wind cavern there was a viper gang encampment right next to it. I couldn't get in there because it was a very hard lock and I didn't have the skill. I have done many play throughs since and remembered it so I went back and know the tunnel structure is there but no door to pick and enter.

Am I mistaken about there being a door there before or did it get nixed with a patch? If so why?

Never an enter-able tunnel there for me (there is a structure, but it's just looks). I'd guess you're actually thinking of the 'train tunnel' that's related to the Boomers.

There are a few train tunnels in the game. I think you can only enter one or two of them, the one near Nellis is the only one I know of for sure. They even have a door mesh. It maybe that they removed the door mesh in the last patch on the ones you can't enter.

If it's the one with an entrance by Nellis, the door was there and marked as a very hard lock in my game the other day. Didn't go in though, lacking the lockpick skill.

Mind, you I walked out of H & H tools the same day, only to find tthe building had completely vanished upon my exit. I could see right through where it had been, but when I tried to walk through it I bumped into the invisible building. Then the game crashed. So the Mojave can be an unpredictable place.

Of the three, that I can remember, only the Nellis - wasteland route had a door you could actually enter.
The one southwest of Nipton just had a lottery ticket left by the grate.
The other next to the Viper gangers never had a door you could enter, not one I saw anyway.