Hello, I don't know if it helps much but I had the reset happen to me also on patch h. I didn't had that many mods enabled, mainly cbbe, better eyes, better facials, better lighting, darker nights, enhanced legendary mods, XDI and unofficial patch. I sadly don't have the save anymore because whatever I tried, the HQ just reset and I thought my game was done. So I try to list what happened and what I found out maybe caused it to happen.
First I did had a save from ss2 before up until the end of the main story for it and I went in on it. It was before all the reworks from what I heard happened. So I went and everything was fine until Lupe. It somehow bugged when I went outside, she was at the store but Jake wasn't anywhere. Not in the tunnel, not sleeping, just gone. So I needed to backtrack the mission (I save a lot for such possibilities) and the second time it worked. Not much happened, besides I thought my game was bugged since I saw that shhandy should be at Concord to recruit me but he wasn't. (I later found out that you need a certain amount of plots in settlements, which I think I had but I could be wrong) I used the console to get the quest with the hostage. After that everything went fine and I got all the missions the one for their new police HQ.
After that I did the main story to when the fight for the gnn starts. (Btw. My game wasn't that advanced I basically went for diamond city and nothing more than that.) I recruited the minuteman and cpd and I went for the 'alarm' option. When it came to the fight in the basement, it was completely bugged. (Don't know the name anymore but the guy that beat Jake in the vault) he just stood there with two gunners, not saying anything. I don't know if it bugged because I thought I went the wrong way first and went back up again right after it first loaded; but again, nothing happened. Talking to him did nothing and Jake also said nothing. After I just shot him and Jake then played his cutscene where he takes his revolver? Idk what it is but after that all went good again.
When everything was cleared I did the how to HQ quest and this was possibly bugged as well. I had 46 out of 60 needed power for the tutorial to complete; then I tried to troubleshoot.
I disabled all the graphic and body mods. Didn't worked. I disabled xdi; didn't worked. Btw I did use the German version which I dropped then also too, but it didn't work either. So all I had left were the legendary mod, the unofficial patch, both German and English (I tried both but not at once) and the mandatory mods for and with ss2 and chapter 2. I also updated to the I patch but it still didn't work.
After a bit of searching I saw that you can somewhat skip it by tgm in the console, so I did. It worked for the whole mission. The concordians went home and I had new quarters build so I came up to 10 in total. That's when I noticed the reset.
In my ss2 normal run i did some side quests for unique settlers, so I went to sanctuary and saw many new faces offering me quests. I did like 3 of them, one ghoul with a space suit, a woman for which I needed to hunt radstags (btw this mission cost me multiple braincells since I needed 2 hours to realize I need to put a sensor in his inventory and not to use the craft able sensor. But I think that's my bad) and a guy with his robot. In my first run I already had a guy that looked like a fat gunner, a Mexican? Ghoul and the space ghoul. I sent 4 guys there and since I had 6/10 places in the HQ it gave me a message that no more could be send there. So I went and looked, only to see that everything was reset. The numbers were all black and the indicator for the supplies didn't display anymore. The entrance was empty and every room was reset. I thought 'nice' and needed to load a save before I send them there. Surprisingly, when I only send 3 instead of 4 it didn't reset. For now. I went a bit through the HQ, everything was fine, I cleaned some rooms and then picked up the Nuka quantum which I forgot. (The one when you go through the entrance, then the main hall the the other end and then left on the bench). I did some new settlement stuff because I saw that I haven't gotten the nightingale quest yet and I knew I had to build like 30 residential plots in my settlements, so I did and got the quest. I did it until the quest for the hospital finished. I needed to wait for the next quest so I went to my HQ again, this time through the roof since a gunner spawned there with a fatman which killed me twice. So I went down the elevator and the UI still worked. I saw that somehow my resources was higher then my limit (I played on the sim city config where you build/upgrade on the 4 resources. I had like 4800 in the first, 7500 in the second, 6400 in the third and 3900 in the fourth, even though I had a limit of 12000) I didn't thought of it much. then I took the elevator up only to see it reset again. Same thing as it was before. I didn't assign new settlers there so I had no idea what happened.
The thing I noticed was that all the loot was reset. The fatman on the second floor, the Nuka quantum I talked about earlier and so on. So maybe the whole reset comes because the engine still thinks of it as the gunner plaza, and just completely resets it's loot and therefore the whole HQ? That would also explain why that lonely gunner and one turret which I forgot to mention just spawned like it was vanilla.
After that I dropped the save and I am currently on doing a vanilla playthrough while I wait for more updates to then put ss2 on after I'm finished. This time I have almost no mods besides unofficial patch and the enhanced legendary mod.
So idk if this helps in any capacity, I truly hope so though. And I'm sorry that it's this massive wall of text for my first post here.
