Odd map behavior after adding second part
I am working on a rather large three-part map. To help keep compile times down, I cut-n-pasted out the first and second parts once they were done. (yes I should have used visgroups) After finishing the third part, I pasted back in the first and second parts (yes I should have used an instance) and now some really odd things are happening. Pictures and descriptions:
In the first room, there are some issues with what I presume to be visleaves. The rooms' two major visleaves apparently don't "see" each other, so I cannot see one when I cross into the other. This is a splitscreen picture of both Atlas and P-Body looking at each other, about 32 units apart. The flag floating in the air is on Atlas' back.
In the second room, cubes do not press buttons. At all. They just chill on top. Also, on a (most likely) related note, triggers do not work. Trigger_multiples, triger_onces, etc, do not fire outputs.
Finally, fog is a lot different, as you can tell by the comparison shot above. The new is on the left, the old is on the right.
I have verified both Portal 2 and the Authoring Tools. A few files came up as failing to verify but after redownloading the problem was still there. Nothing of interest shows up in either the compile log or the in-game console. All in all, this has me really stumped 
I would really appreciate it if anybody could throw out a few suggestions on how to fix this. I can upload pretty much anything required, whether that be compile logs, or the map source, or anything, really.
Thanks in advance for your help!
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Man, seriously?? 
did you eventually get everything snapped to the grid after that maneuver? I'm sure you didn't, even if you used the "Snap selected to grid" tool.
Some advices for this:
1. You NEED to learn how to use the cordon tool. This is very useful to isolate certain areas from your map that you need to see compiled without compiling the whole map each time.
2. Even if you don't use visgrouping, you still can use hide/unhide (pressing the 'h' hey will hide what's selected / 'u' key to unhihe) to hide stuff...
3. I'm not sure if you already know about this button, but there is a button to make hammer to not draw the wireframes of your models... 
(it's the fifth button from the right side of your hammer toolbar). This should help you some with visibility while mapping.
About your problems, hehe, due to that bad maneuver you performed >.<, it can be due to a many possible issues. Of course you seem to have a problem in the vislaves created since depending on the players position some objects are being rendered and some others aren't. But, maybe it's just that the level is a bit too large and by default only certain number of visleaves can be rendered at time in order to preserve a good performing in game. Try to use a func_viscluster to see if it helps out. Also, check out the visleaves that were created by going to your Menu > Tools > Load Portalfile while you are in hammer with your map loaded... even though you think there are "2 major visleaves (portals)" I'm sure you'll have a bunch more of them 
Hehe, don't you see that you created a button frame brush with no hole in the middle for the button? it is stopping the cube from pressing the button completely 
About the fog, all I can say is that the env_fog_controller is one of the most sensitive entities in Source. In your left picture it is not showing at all. For it to show up properly you need to make sure that your map has not any single leak or any model outcoming from your map's bounds: depending on how much a model is outcoming from the map walls, you'll get the compile to work out but some issues like this can appear... Look into this.
Good luck 
useful tools and stuff here on TWP 
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If there are multiple env_fog_controllers they can fight and stop fog from showing up. Did you have one in each of the three parts?
did you eventually get everything snapped to the grid after that maneuver? I'm sure you didn't, even if you used the "Snap selected to grid" tool.Good catch! Upon further inspection that part is very slightly off-grid. I made the chambers I cut an instance and defined a func_instance_origin, but now the instanced chambers are way above where I put them when I compile. Stranger and stranger...
I would have used cordon in a heartbeat had it been an option. Unfortunately these chambers are "inside" the other (difficult to explain) so unless cordons can "exclude" parts of maps or I can define multiple cordons this wouldn't have been possible.
The room is actually pretty simple; thus there's only about 4-5 visleaves in the room, and only 2 touching that could cause that problem. I think a func_viscluster fixed the problem but it is hard to judge because of the problem I had above with the position of the chambers.
The odd part is this instance works in other maps without a problem. I will look into it but I have a feeling it's more the fact that triggers don't fire outputs (which I would say is the more major problem 
) If you are joking disregard this
There's multiple env_fog_controllers, in the global ents instance, but only one of them is activated. There is a small amount of fog, it is dark and very sparse. It's also probably really hard to see from the screenshot I posted.
Thank you both for your great responses! I may just end up splitting the map into two parts since it's becoming much too large to deal with, but I would prefer to keep it in one part.
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Func_instance_origin only defines the origin for VBSP. In Hammer the origin stays at the origin. It's a very annoying entity.
I've seen this behavior before. It's a flipping pain.
It has something to do with visleafs and generally shooting portals fixes it. Also the distance between the two players totally influences what's going on.
You could try various things here; block off other areas with areaportals; put a viscluster in the room; shrink the size of the room by using a 3d-skybox etc.
) If you are joking disregard this easy fix: give the instance a name
profit!
as for the fog; I have no fogging idea.
It has something to do with visleafs and generally shooting portals fixes it. Also the distance between the two players totally influences what's going on.
You could try various things here; block off other areas with areaportals; put a viscluster in the room; shrink the size of the room by using a 3d-skybox etc.
Ah, that's kind of what I was thinking. Glad to know this issue has been seen before! I will almost certainly just split the map in two instead of dealing with this crap
profit!
I must've not said what I meant here. All triggers do not fire outputs, regardless of whether or not they are instanced or not. This is map-wide and affects all triggers.
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