A variety of questions
This is my bet: I think that when you changed that observation room for a different one, you didn't care about the inner items and their names. Each observation room uses to come with an env_ projected_texture which is a special entity as you can't have more than just 1 active at the same time into your level. Surely this entity was triggered somehow and now maybe your map continuous looking for it to lighten it up but fails...
You mentioned you only changed it for a standard one and that you removed any, but have you tried to place again that one you added in the first place? in the case that it was placed into your map automatically, can you remember the name/location of that first obs-room? Try to place it again and see if your map works again...
And if your map works again, try now to modify THAT observation room visuals (textures, glass, even window frames...) but leave the rest as it comes.
I tried changing the vmf back to the p2editor observation room; it didn't help. Keep in mind that all I did to change it to the standard observation room was change the vmf filename, so the fixup name should be intact from the editor. Is it supposed to be observationroom2 by any chance?
Edit: On another note, even though I've been saving periodically by pressing Ctrl+S, when I close the program, it asks me if I want to save my changes. Maybe it hasn't been saving properly? Or does it always do that?
The way you describe it it DOES sound like a problem. I made a thread about this behaviour: puzzle-creator/how-to-reimplement-the-pti-elevators-after-hammer-polish-t6371.html
Move the camera inside the entrance elevator. Doubleclick into the orange "blob" that's filling the whole elevator. That's the func_instance combining all the stuff happening in the beginning. You should see the Class Info now. See the second entry from the top: $no_player_start. Change its value from 0 to 1. That should do it.
Edit: It might be necessary to also do this for the entrance room. So doubleclick into the orange "blob" that's filling the whole entrance room. Change the $no_player_start value to 1 here, too.
Note: If it happens to you that after doing this and compiling you suddenly start in a black room without a portalgun, this helped me: Save and close Hammer, open it again and load the map, compile again.
And while editing my latest map in Hammer, I found that this last problem might have to do with having something of the map at the origin (the point where the x y and z axis meet up). You could try to move everything away from it.
The way you describe it it DOES sound like a problem. I made a thread about this behaviour: puzzle-creator/how-to-reimplement-the-pti-elevators-after-hammer-polish-t6371.html
Move the camera inside the entrance elevator. Doubleclick into the orange "blob" that's filling the whole elevator. That's the func_instance combining all the stuff happening in the beginning. You should see the Class Info now. See the second entry from the top: $no_player_start. Change its value from 0 to 1. That should do it.
Edit: It might be necessary to also do this for the entrance room. So doubleclick into the orange "blob" that's filling the whole entrance room. Change the $no_player_start value to 1 here, too.
Note: If it happens to you that after doing this and compiling you suddenly start in a black room without a portalgun, this helped me: Save and close Hammer, open it again and load the map, compile again.
And while editing my latest map in Hammer, I found that this last problem might have to do with having something of the map at the origin (the point where the x y and z axis meet up). You could try to move everything away from it.
So...this pretty much occurs randomly when compiling? Because that's what it seems like.
That's what it seemed like to me, too. But after I moved everything away from the origin, saved, closed, opened again - it never happened again.
Cool, so I just got everything in my map to disappear with no undo. Doesn't reappear after re-opening. That's cool. All I did was move the camera.
Any idea how I did that so I can avoid doing that again?
Edit: On second thought, I might have accidentally hit H.
Edit 2: Alright, moving everything away from the origin seems to work. I even changed the observation room and it hasn't thrown up on me. Thanks, zivi7.
Glad it worked for you, too. 
OK, so I tried to add a prop_static, and Hammer crashed. When I re-opened Hammer, I tried to reload the file, and it crashed again. After a couple times of this, I just used the open dialog to open my map, and here's what's left of it, apparently:
The rusty frame model is just one of the skins of the clean frame model. They are called square beams, and you can find them by searching in the model browser: square. All the different sizes should come up at the top. Once you've set that model as the world model of your prop_static, change the skin to 1 for rusty and 2 for blue. If the skin is 0, it will be clean and grey.
[spoiler][SP] Alternate[/spoiler]
you may have figured it out by now.. but I dont feel like reading everything
the mandatory observation room is mandatory because it has some vital logic relays, last I checked, I recommend building your own elevators from instances, especially if you want to go with the overgrown theme
I also recommend you learn how to use hammer for normal map making before you try to jump to the fancy stuff IE. detailing.