Looked at this way, the coffee cup, when given to Cooper initially, is strong and closed off. Then it is weak and vulnerable to be opened. Leland said that BOB opened him, Leland invited him, and then BOB went inside. BOB uses fear to open people in order to get entrance. I think that the coffee also becomes oil to show that Cooper will be possessed by BOB. This is why the MFAP says “Wow BOB Wow” followed by “Fire Walk With Me”, which has always meant possession by BOB to me, because he knew from this that BOB would get Cooper. Of course, Laura already knew this when she told Cooper that she would see him again in 25 years and then gave the sign language for a tree, after having said meanwhile. After Laura’s face turned into these specific colors, while talking to Harold about BOB wanting to be her, she said “The trees, the trees”. The meanwhile she referred to was the 25 years Cooper would spend possessed by BOB. This is also why her doppelganger is screaming at Cooper. Laura hid for years her fear of BOB and his presence in her life from everyone. Cooper will soon be BOB. Dale also will attempt to change the past by making Laura possessed by BOB instead, something Laura was willing to die in order to prevent.

You ask why BOB would trade Wyndham’s soul for Cooper, keeping Cooper alive. I think we have the answer in FWWM. This is hinted at during the ending of the TP series finale when we see Laura’s face in the coffee during the credits. If the coffee is representative of some test Laura is going to be facing it again. There are things in FWWM that happen at the end of this ep: Annie and Cooper in Laura’s dream. The script to FWWM also hints at this travelling between future and past.

I think that BOB wanted Cooper to tell Laura not to take the ring that Mike wanted her to have. The ring saves Laura from possession and it was what saved her in the past. I think that she was meant to have the ring from the moment in her dream when she has it in her hands. However, because of her fear, Laura did not take the ring at this time, altering the past. BOB wanted one more chance at Laura and by Cooper being in the Lodge he got it. This is the canned corn that Mike/Phillip references being stolen during the traffic jam, the pain and sorrow caused by Laura’s death. Luckily, Laura did take the ring when Mike rushed to the traincar that night and threw it in. BOB/Leland was too busy assaulting Ronette and closing the train car doors to notice and the Angel freed Laura’s hands so she could take it.

I think that BOB used Cooper’s regrets about Caroline and feelings for Annie to get him to tell Laura the wrong advice. Cooper was willing to sell his soul for Annie and vowed that another woman would never be hurt by him again. If he could get Laura to not take the ring and BOB to possess her he never would have come to Twin Peaks and Annie would be safe.

There is also the darker reason that Cooper was a coward. He runs away from his doppelganger even when Hawk has warned him not to become afraid in the Lodge. FWWM has always been linked to the poem heard throughout the series to me. Cooper is the Magician, looking through future past for his one chance out between 2 worlds (Note the finale is called Beyond Life and Death: the 2 worlds) and BOB’s potential possession.