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This is how I interpreted the scenario, so if I am wrong please tell me.
When Desmond was in the helicopter and went back to 1996, his memories of 2004 were erased because of the high exposure to radiation when he turned the key in season 2 (or was it season 3?) . When Desmond left 1996 and returned to the present, it was like he just arrived and has no memories of the last three years. The only way to regain all his memories from 2001-2004 is to go back to 1996 and find his constant, which happens to be Penny, and tell her not to change the phone number so he can call her on December 24, 2004. When he came back to the present, December 24, 2004, he called the present Penny and made contact, which then brings back all his memories from the past three years. I think the time travel ended once he made contact with his constant.
This is like memorizing a formula!
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