An update just now. Our server restarted again, I put down crafting stations and structures 30 minutes before the restart. Every structure is gone, the crafting stations with everything inside stayed.
FUNCOM. Fix this. Your game broke with the latest patch.
You donāt have to use the exclusive parts of Age of Cal. Age of Cal is a major overhaul mod that touches virtually every blueprint in there. It was recently updated, so obviously you want to ensure that you are using the most recent version. Warrior Mutator also touches a lot of stuff, so you might want to try without it, do a server reboot, and see what happens (though I think the author said it was compatible with the latest update).
Pippi also has a ton of issues right now until the pippi team can update it. Not sure about Pickup plus, but wouldnāt surprise me if it wasnāt compatible at the moment since it involves every item in the game. Bottom line, try without all mods, put down a bunch of buildings or whatever, reboot the server, see what happens.
This was already tested as the server wiped. It was a clean wipe, no mods. As Age of Cal. updated it was added, then a day later (today), mutator and the rest was added. - Pippi has been part of it all along since itās a roleplay server, and Pippi is just a must for text based roleplay.
Iām keeping options open. But thing is, how would Pippi cause buildings to dissapear? It could crash the server, sure. But all of the commands are already disabled to prevent that.
Outdated mods are unpredictable in what happens (Iām a mod author, I know this very well). All I know is that this seems to be an isolated issue, very few on an official server has had their stuff disappear over night since the patch dropped(well, other then the on going bug that may or may not be related to decay), or else the forums would be blowing up. So if itās happening to just your server, or a few servers, whatās the connection there? Trust me, Iām a builder, so I fully feel your disappointment and frustration.
After the full wipe and you had every mod turned off, did anything disappear at that point after a server reboot?
Pippi is not up to date. Pickup+ has not been updated however, since august 14th or so. And Fashionist, which doesnāt really add anything major to building, hasnāt been updated since july 4th.
So it could be Pippi, Pickup+, Warrior Mutator or AoC. Though the official AoC server, which is run by the modās dev team, has no issues at all. So that crosses AoC as a single mod off the list. It could be a compability issue, maybe? Or Pickup+ which affects literally all items in the game, though it includes crafting stations and crafting stations DO NOT dissapear.
Warrior Mutator has also been updated. But other servers having Mutator donāt seem to have any issues either.
We donāt have AoC but had the building problem, so it could cross AoC off the list indeed.
However, we do have Warrior Mutator, Pickup+ and Pippi.
well the one thing i feel most of us has in common here is pick up plus and or unlock plus. so anyone that are good with testing things out, i would check out those 
Those who had the building parts disappearā¦ do you have the āpick up building partsā functionality of Unlock+ (with pickup) activated?
We use pickup+, not unlock+. But we do have the pick up building parts functionality, yes.
https://steamcommunity.com/sharedfiles/filedetails/comments/877108545
It looks like Unlock+ (which we use, I didnāt think we did but apparently we do), is the issue. Everyone should remove the mod until itās updated.
We just tested this. We removed unlock+, which caused structures to dissapear. But then we built structures after the removal, and restarted the server, and structures are still there now. Unlock+ is the culprit of structures dissapearing.
Yay! I mean crappy that it happened to begin with, but yay that you found the source and a solution!
Same issue is happening on the private server I play on. Yesterday I built a medium building out of reinforced stone and filled it with barrels, a table, two hanging brazers and two crafting stations. Then I build a massive defensive wall out of Aqualonian pieces on the other side of my base and when I logged in this morning POOF! they are ALL goneā¦every piece. Another player had her gate, gate frame and surrounding foundations go missing. Itās like these Funcom guys make a game out of Fāin up. Who can add the least amount of content and break the game the most.
Any mods as well? In CookieJars case, Unlock plus was the one causing their issues.
We tried without Unlock+ and restarted the server. The buildings were all there in the database, no problemā¦ But as soon as someone approached the buildings, they all got destroyed.
Looks like Unlock+ was a good idea, but itās not that, at least in our case 
It would also explain why some people were encountering the issue on Vanilla servers with no mods.
Existing structures might still be driven by unlock plus. With it gone, they them blow up (Iām theorizing). For funsies, try a new structure, followed by a reboot.
What other mods are you running? There could be others causing this issue as well.
In our experience, all buildings that were built during the period that we still had unlock+, the moment Unlock+ was removed, all buildings built in that certain period got destroyed. But the buildings that were built after Unlock+ was removed, stayed every restart. No building has dissapeared ever since.
Just for funsies, is your decay turned on? There is a discord user who says they are using Unlock plus as well, but didnāt have issues from the patch with buildings blowing up. Their decay is turned off.
Our decay and purge was both turned off. Unlock+ removal magically fixed it.
Alright, so much for that idea then. So somehow itās still linked to Unlock plus, just not entirely sure what other link there is that makes it so some people are okay, and others are not.