Recently, my safehouses on my main character have been disappearing. I am playing on PS4 and have most, if not all of the safehouses unlocked. Every time I load into the game, a portion of my safehouses disappear off the map. This happens both in multiplayer and singleplayer. I have all of the safehouses unlocked on Himfjäll island, but every time I load into the game, I only have Himsundsbryggan and Björntunet Hotel unlocked. I also have all of the Archipelago Region safehouses, but sometimes I only have Yttervik, and having to go unlock them all over again is really annoying.
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Yes. That’s a known issue for playstation since landfall update.
The devs are aware of it and look for solutions to fix it, but as far as I know, they haven’t found the reason for it yet.
I’m living with this for almost two years now on my primary world.
My second world isn’t affected yet, but my progress there currently is stuck at building blocks mission.
Ah, okay. Thanks, I thought I was the only one affected.
same here 
I get this glitch also, it’s a strange one
Same, except in my case all but 9 bunker safe houses disappeared and have never come back.
I’m playing the ps4 version on the ps5 and i just ran into this 2 days ago. Last thing i was doing was exploring the mountain region on my main and only world. I think i even lost some locations permanently too. An example, i lost the Angeras church location marker.