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.
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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