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I don't know why the index_pos is pointing there, is it possible that you're mistaken about this? I would expect it to point to the index data records.

The reason the connection records are replicated in the index is so that you don't have to load all the chunks to know which connections were recorded in the bag. They are left in the chunks because they need to be written when in encountered and removing them would require rewriting the bag data (the index doesn't exist until the bag is closed or reindexed after a crash). Also, writing the connection records down when they arrive makes it possible to see connections appearing and disappearing in time.