It seems like mass placed blocks disappear after a while. Many of these blocks arent in areas accessible to enderman.
the bug seems similar to the "ghost blocks" but sort of the opposite.
An example, to describe it a little better, I recently built a custom mountain in survival and after a while a few of the dirt blocks have disappeared over time and has left holes throughout the mountain in random various places.
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Most of the areas are in steep wall-like areas where enderman cant spawn or stand, I'm fairly certain that enderman are not involved but I will further investigate on peaceful and see if the issue still occurs.
I try to patch up most of the holes that i find, but heres a few. Like i said, these areas dont really seem accessible to enderman and I have recordings of me placing the blocks so its not places that i have forgotten either.
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Enderman can pick up dirt blocks (also variants of them like coarsed dirt, grass blocks, ...). Are you sure it is not related to enderman?