I'm in the middle of making a mod for the Thieves Guild that overhauls the Cistern. Let me just say that this is an annoying first mod to make due to the potential to break the questline. Anyways, I am running into some problems with some of the items. The way it is set up in the creation kit, many objects in the cistern are tied to those red X's, the markers, TGStatusGuildStage 1-4. I don't know what initiates one, but I know that everything tied to 4 is supposed to appear after completing the final Special quest. I would assume 1-3 follow the respective SQ as well.
Here's where the problem comes in. Certain items that are not supposed to be there until 4 are showing up in game before 1, these items are causing problems for me. I am also trying to set certain items to disappear at certain stages, mostly random pottery, baskets and hay piles, to make it seem like the guild is being cleaned up as it grows. But these items are not disappearing.

I made sure the items were static, set the enable state to the stage I wanted them to disappear, and clicked the "set enable state to opposite of parent". I assumed the parent would be the enable ref, so my understanding was that when the Guildstage 3 ref hit these objects would be disabled. I was wrong, but now I am at a loss.

Help on this would be greatly appreciated. This problem I am having has also blocked off some new areas of the cistern that I've added since the walls won't vanish when I want them to.

EDIT: Yes I did a google search for this, but a more detailed search came up with nothing, literally nothing, and a less detailed search just comes up with bugs people are having.

Make sure all the objects that change from natural progression (the way Bethesda set it up) actually have enabled parents; if they don't then Bethesda activated everything some other way and those XMarkers might not help you. Then, if Bethesda did use parents, make sure you know exactly how/when/where those parents get activated; Bethesda really tried to make sure you couldn't break the quests, so often there are numerous way to advance the quest stages, so there would also be lots of places for parent states to be enabled/disabled.

Next, how are you trying to enable your objects? My recommendation would be to do it in the quest stages papyrus fragment area (or dialogue I suppose), but I haven't ever changed the base quests at all, so idk if the .esm editing issues would matter for you (certain parts of esm files can't be edited and show in-game without some trickery).

Well, I took my idea from how Bethesda set it up. In the Ragged Flagon there is random junk in the new merchant areas that are replaced by the merchant property as the questline progresses.
However, upon closer look, I noticed a difference. In the Ragged Flagon, under the Enable Parent tab, the reference is TGStatusStage(one through four). In the Cistern, the reference is TGStatusGuildStage(one through four)Ref. So to be honest I have no idea what the GuildStage ref is, as the StatusStage from the Ragged Flagon is related to the SQ from Delvin. So that is my problem. Do those markers work if the ref is in a different cell? Or how do I find out exactly what marks each stage, because then I can set it up properly.

EDIT: Since I'm on the topic of enabling/disabling things, what activates the safe in the Cistern. It says initially disabled, but I'm not seeing what enables it and I've never encountered it in a game.

Yes Markers work across cells (Ex. I have markers in my mod interior that activate smoke outside in the Skyrim worldspace)

The GuildStage ref could be the little collectables (I'm guessing)

This is why most people don't like doing these type of mods. You have to go through the quests (stage scripting, dialogue scripting, etc.) just to know how everything is working. From looking a little bit, it seems like those markers in the cistern could work the way we're thinking though, so make sure you try doing this from basically a brand new save to test your stuff, as it may have worked, just not the way you were hoping. It looks like a bunch of the "quests" Bethesda have for the thieves guild start right away when the game starts (behind the scenes), so loading a save after that wouldn't reflect your changes if the script affecting those markers was already in place.

As for enabling/disabling things, it could be anywhere really: Quest papyrus, quest dialogues, quest scenes, some random triggers out in Skyrim somewhere, switches, and the list goes on really; though I would guess quest stage or dialogue/scene scripting (Bethesda doesn't leave many triggers in the game). My first step would be to replay the thieves guild quests on a fresh character, and note EVERYTHING you can about the order of things happening during the quests, when things appear, etc. so you can at least narrow things down somewhat. Then I'd go through each quest in the CK with TG in the name and try to understand what they all are doing, again to rule things out, and finally just start chipping away at the list of candidates. For any scripting in the list of candidates, look in the properties and skim that list for references to the XMarkers (they might not be named exactly the same in scripting, so you have to do it in the properties).

Good luck, you picked a difficult first mod I must say!