Ender pearls that are suspended in holding chambers via use of honey blocks and upward bubble columns do not teleport players under certain conditions: 1). The player who threw the pearl is in the nether, or 2). All players leave the world and then log back in.

It appears that the second issue is caused by ender pearls losing all data when all players log out of the world. This issue can be demonstrated by opening a standard 1.16.20 creative world, throwing a pearl, then leaving the world before it lands. When the world is rejoined, the pearl can be seen falling to the ground and disappearing without teleporting the player.