He was instructed to do so by Rock Newman, who did not want to do business with the WBC and Don King because of their shady business practices. He was acting on behalf of Newman, who was essentially telling the WBC to go fukk off.
Bowe was never afraid of Lewis, and always wanted to fight him. In fact, Bowe and his camp made offers to Lewis after the trash incident on 2 separate occasions...
1) They made an offer to Lewis and his camp in 93 for a unification fight (Bowe still had the WBA and IBF belts). Lewis was guaranteed 11 mil and a 50/50 split if the purse went above 32 mil. Lewis and his camp turned it down and opted to fight Frank Bruno & Tommy Morrison instead.
2) Bowe and Lewis reached an agreement in late 94 to fight in 95, provided that Lewis got past Oliver McCall. He proceeded to get KO'd, and the fight went up on smoke.
The notion that Bowe was afraid of Lewis and was ducking him is as silly and untrue as Mayweather ducking Pacquiao