Hi,

I've placed the first three essence stones and got a cutscene with the stairs rising but they dropped down at the end.
Having received the fourth essence stone I cannot place it because the altar is also lowered into the ground. :-(

Any ideas or do I have to start from scratch?

Hey bud, do you still need help with this after three years?

Probably not, but it could help the others:
The puzzle involves placing the idols in correct temples (and possibly in correct order). If the placement doesn't meet the criteria, the cutscene of raising and falling the stair will play. Then you can pick up the idols again from the cavities, even though they appear invisible, and start over.