Wtf?!
Now most of my safehouses are gone, too. 
Just 16 left. And… When I startet my game a few minutes ago there came multiple messages “safehouse unlocked”.
Edit 1:
I quit the game and restartet it… Now there are just 11 safehouses left. 
Edit 2:
Ahhh. And ALL locations are gone.
Edit 3:
I downloaded the newest safe-file from the cloud backup of ps5… Now everything looks fine again.
That was probably scarier than the Texas Chainsaw Massacre… 
I haven’t had that yet myself, but I have many game saves saved just in case.
So do I, but that didn`t work.
Today me and my friend had the same again and now I’m sure…
WARNING
Don’t visit Karl-Erik lighthouse!!!
It’s actually the only savehouse which is gone in my game. Happened after landfall update. The day after unlocking it again, almost all of my savehouses and all locations were gone. This happened twice for me and once for my friend.
Sorry for double-posting,
But it happend again… Without traveleing to Karl-Erik lighthouse. Almost all safehouses are gone. Every time I fast-travel, I get multiple messages that a new safehouse was unlocked.
Now I don’t know what I did wrong.
Even downloading a backup from the cloud doesn’t help any more.
This time all other locations are still present…but there are just 17 safehouses left + my homebase.
Edit: seems a bit like the still existing safehouses could be mission-related ones (i.e. all command-bunkers are still there).
Just a little update:
I recaptured the safehouses in the starting region after it happened, saved and took a look at it yesterday.
Two ones of the recaptured safehouses are again gone. Yesterday I recaptured some in the farmlands. I will take a look today what happens this time.
There are still multiple messages that I "unlocked a safehouse on game start.
Btw, yesterday I used my 3rd character (to get the xp of recapturing the safehouses) and I" was able" to unlock the airfield safehouse 3 times (and got the xp for that 3 times).
Somehow it’s a bit funny… Like a feature. The machines seem to get control of a region again and I have to recapture it. 
But this time I indeed would like to have a faster vehicle than just the bike. 
Edit:
Ah one more thing. It seems that I lost a skillpoint, too. Two days ago I earned one for level 10 and spent it on first level of carry weight. Yesterday, when I became level 11, this skill was gone… And the skillpoint as well. I spent the new one again on carry weight and will see what happens today.
So, got some response from todays livestream that the devs are aware of this issue and are working on it… Good news!
Working on it that it will not happen again or that the disappeared safehouses are there again, too?
I have no idea. I think we’ll just have to wait and see, my guess is that we will have to ”unlock” them again manually.
That is what I’ve done since it happens. I just finished archipelago and farmlands. Just two safehouse got lost again since I startet recapturing them…
I had an idea earlier for the end game: that the machines would be able to retake the bunkers and/or safe houses…
With your hands on experience, do you think it would be a good addition to the game? 
Yes, it is, for lategame or as an additional source for xp for new characters.
Of course, a few tweeks are necessary:
I just wanted to mention that this problem still exists.
I hope it will be fixed today but don’t see much chances for that.
Again:
I had all savehouses discovered for many months. One day, after landfall update, one savehouse suddenly was gone (karl erik lighthouse).
After recapturing this savehouse the real problems just began. Next day suddenly almost all savehouses but 17 were gone. I loaded the backup from the Playstation cloud and at first everything looked fine. But the problem returned.
Now I’m still recapturing as many savehouses as possible each day, but every day some of them disappear again. (i. e. I had to recapture the airfield at least 6 times).
It would be great to get a solution or a fix that it never will happen again.
It happened again.
Almost all but 13 safehouses are gone: 
Edit:
I’m excited.
I reported this issue to the support today and attached my savegame.
Just short after that I got following answer:
Generation Zero - A Support agent has deemed your ticket #169075 Solved!
Your Generation Zero ticket here has been deemed Solved by Support. If you have additional issues you would like to report, please open a new ticket.
Max (Generation Zero)
Apr 25, 2022, 16:01 GMT+7
Hello Madchaser84,
Thank you for contacting Generation Zero Support.
Thank you for taking the time to report to us. We have submitted the report to Development team successfully, the team will actively investigating how this can be resolved with high priority. We’re really sorry it made your experience with the game less than what we intended.
You can also view our known issues to see which things we already know about and are working to fix!
I hope that you can continue to enjoy playing Generation Zero in the meantime.
Generation Zero Support
Status update:
I lost them all again, even the backup of my savegame doesn’t help.
As you can see in the second screenshot I unlocked 279 safehouses yet… As I don’t play online with others… Those are all mine, but multiple times unlocked…
I was so glad that i can play gz on ps4 again, but now there is a new problem. I have lost almost all Safe houses except from the Bunkers and a few on Himfjall and the worst of all, sometimes they disappeared again although i have retake the Safe zone, meaning that even if you recaptured the Safe zone, you have a chance to lost this again. Please fixed it. I have freaked out by discovering this.
Moved to relevant thread.
//Mod
Hello again,
Now that I played a few days in a row again, destroyed most fnix bases and recaptured some of my safehouses, I really thought that my game is on a good way. Until now.
I just started the game and had to see that again I spawned at Yttervik. All safehouses, but the mission related ones, are gone again.
Maybe it’s connected somehow to Apex connect? I did some assignments yesterday… The first ones I did for a long time now. I got rewards and some resistance-points. But that’s the only thing I did differently to the other days.
My map, filtered by safehouses:
My log, unlocked safehouses:
Please, fix this. Please.
Hey @Avalanche_Pontus, is a solution for this issue in sight, too?
It’s now, for me, since febuary (Landfall-Update) that almost all of my safehouses get lost every week.
Me too. Every time i reach over 78 or 79 save houses, it dissapear and get back to the called numbers.
Is it related to playing multiplayer?
Or to some specific safehouses?
Or to the assignment system?
For me it doesn’t matter how many safehouses I recapture. 5 or 50…they all fall back to the above said.
