I think I’m stuck. I got the Graveyard Key and, after clearing all the tentacles, I went to Sacrament to use it. After opening the door, I was able to loot the same key again.
Then, when I returned to the Graveyard, the door was locked again, so I used the key a second time.
Now, all the tentacles have respawned, but the spores have not. Additionally, the Graveyard door is locked once more, you can see the chest behind it is already open. 
i wonder if this is intented that doors lock after location restet, i have got the same problem.
Today I played again and everything had respawned, including some ladders I had already pulled down, so I had to activate them again.
Thanks to that, the spores also reappeared. However, the Graveyard door is still locked.
After the second hotfix, I was able to open the door and it remained open.
Some issue here. The polips are back but the spores are not respowned 
My primary realm has everything unlocked. After the Together patch, i noticed something different. The bridges in Marin woods were reset, meaning they were not in the down position ( i can cross them), they were in the upright position.
All bridges throughout the area. Kicked them down again and all is as it was
Ya I noticed the same thing.
Hey Darc,
Did the bridges stay down after you kicked them down again?
Silas
Yes
One time event
Also noticed it happening with some ladders across Sacra. Again, one time event and not every ladder.
Alas I can’t remember which ones
For future reference, this is most likely a consequence of Moon Studios updating the area with their main patches.
In most cases, Moon will not support Realms that originate from before such changes.
You will have to find soft-fixes or start anew.
Silas