So as I tend to like to do, after completing the story mission at the pyramid excavation site (the one that used to be the Abandoned Archaeological Site POI) I turned the pyramid into a base. Added storage, production, a garden plot behind it, several turrets to defend it, a teleporter, and an SV pad next to the main stairway. I also spawned in one of my CV landing pads next to the site. This had been working fine for several days, and even survived the last two minor patch updates without incident. Today I teleported over from Sigma Fulcrum (yes, I took over as per the story prompting) and the entire base is gone, leaving behind a gaping hole in the terrain where it used to be, complete with the parts I removed to seal the environment. My CV pad is still there where I left it, and even the 3 O2 generators I left outside the pyramid are there, and my waypoint marker too. Everything else is just gone though. I'd file this as a bug report, because it's happened to me before when taking over POIs as bases like this, but I can't find the other report I know was here and obviously since this happened out of the blue I can't give you a means to reproduce this. I just know that due to the nature of the perpetually saved world state, that pyramid base is gone for good and I'm not getting it back. Not to mention that if I want to continue this now broken playthrough, I'm gonna have to cheat spawn a warp capable ship to get back out of the system with - then hope none of my other bases decide to poof out like this. I have no idea if the current state of my game would be of any help, but I'll keep a backup copy of it handy just in case while I pick up the pieces and try to figure out what I lost from the base storage. Oh - I should note that when I teleported to the base, I landed 2.5km away along the equator and not on the site of the actual base. I had to fly over in god mode to get there.
Only thing I know from experience is that after a story POI gets updated in a patch and if you want to deal with it in any way, then you better start a new game and transfer everything you have from your old game into the new one (there is a video from Spanj showing the exact procedure). Failing to do that every strange malfunction - including your story - can happen. Resetting the playfields was not enough in my case when the Sigma Fulcrum didn't appear in the supposed system, it turned out that I had to restart new to make it appear - because the POI has been updated well after I started the game longer ago. This is not exactly the same what happened to you, but the principle should be similar. Now, while transfering your ships from one game to the other with all their containers, locker contents etc. is easy enough, transfering a lot of bases is a real pain. I can only hope that in the future the devs will find a system to make updates without screwing-up old savegames everytime, especially because I can hardly prevent Steam to update the game without me being offline all the time
Looking back on it, I probably should have been deeply suspicious of things when I teleported into Sigma Fulcrum from my teleporter relay and ended up in deep space only to find the POI 9km in the opposite direction. When I got there everything was as I had left it, just in the wrong place. Which, once I "discovered" it again, resulted in there being 2 Sigma Fulcrums on my teleport menu. So I had to rename the working one to make it clear it was the real one. I have used the methods Spanj outlines in his video in past updates before btw, with total success. I just didn't do it this time when the update from 3384 to 3389 happened. So maybe this was to be expected and it's a done deal for this playthrough now. In looking at my backup files from last week, I can see one thing that's certain. The pyramid used to be in the 2904 folder under "Shared" but in the game that's now screwed up, that folder has been completely deleted. Since I had nothing to lose, I copied last week's backup file into the same folder. All of the changes were wiped out, but the POI did reappear where it should be - just not owned by me and reset to its original state. Meaning I'd have to go kill everything inside all over again, and make all the changes I had made all over again too. It's extremely frustrating to have to find out the hard way that it's necessary to start over after every minor update when this is what might happen. And now if I do I'm going to have to just god mods all my stuff back and spawn replacement bases and ships from their blueprints. It's not an easy thing to transfer assets from a long running playthrough. The more you build, the worse it gets, and at some point it's no longer worth the hassle to try and get it all back each time.
Not sure yet, but if you never have visited a system and then you do it and play the POIs there, then maybe it's not necessary to start new; but everything already visited may be concerned by updates, story missions, factions, grafic changes on planets etc. You need to follow the patch notes carefully and make savegame backups in a regular fashion.
The patch notes gave no indication that this sort of thing was a possibility. What I find really telling is that the folder under Shared where this POI should have been was deleted entirely by the game for some reason. Yet somehow it knows 2904 should be there because when I recopied that folder from an old backup, the POI returned but it was reset to original state.
This is a real drag. I feel your pain! I knew I had seen something about disappearing stuff, so I did some looking and found this Tool I'd seen before: https://empyriononline.com/threads/tool-empyrion-wheresmystuff-fix-vanished-ships-and-bases.96806/ I never used it and don't know if it's updated enough to handle 1.5 but you might give it a try ...
I ended up just trashing that whole run. There were other problems besides just the pyramid. Sigma Fulcrum ended up duplicating itself twice, so there ended up being 3 copies of it in the same system, all at different coordinates. The base I converted on some random alien world to use as a teleport relay also ended up axing itself. So something clearly went very wrong, and it all started when the pyramid got deleted.
Ahhh, yeah. Sounds like a Kriel Commander took a swipe at your files, for sure. Sorry to hear that. Life with computers. I'm in the middle of rescuing a crashed Dell laptops' SSD for a client. Suddenly decided it didn't want to remember it's partition layout ... Fun.