Go back and watch the Pearl Orientation film, or the episode where they find the Pearl...
A few things to take notice of:
Chang's arm is totally fine in that film, yet it appears that the film is made AFTER the swan is completed as you can see on one of the video monitors - there are two people at the Computer Station in the Dome of the Swan.
This means the Swan was built and Chang did not encounter any kind of injury to has hand/arm from "The Incident" where the drilling rig collapsed onto his arm, Miles frees him and tells him to run as far as he can.
The Pearl itself may have been the actual mental experiment to observe to the observers - since obviously the Swan did in fact have some kind of a problem and did actually require the button to be pushed every 108 mins...
Why were the notebooks just dumped out into the jungle? I don't think Dharma would've gone to all the trouble to build the Pearl for no good reason, most likely a building was planned to be built to receive the notebooks, and it was never built.
Bottom line is the Pearl video shows that there is yet another variation in the timeline that exists, this would cancel out that there has been a never-ending causality-loop running in time.