Probably the most advanced duel in Screeps ever.

Let the battle begin: https://screeps.com/s/cErsca
W14N1 cleared: https://screeps.com/s/FjCZTQ
Battle in W14N1: https://screeps.com/s/LAz6Mb
Battle in W13N1: https://screeps.com/s/gPA3Lm
Battle in W14N3: https://screeps.com/s/EzGeBI
Meanwhile... Vision counterattacks: https://screeps.com/s/LgpmlQ
Trying to get through the siege: https://screeps.com/s/5HcqfY
Trying again: https://screeps.com/s/bHejTv
And finally: https://screeps.com/s/cp2rEq
W13N4 cleared: https://screeps.com/s/h5vkTz
W14N3 cleared: https://screeps.com/s/k5gk6s

I experienced the same issues. Looks like the global object is indeed preserved, but not every tick. You may try to add some checks if you prototype is already extended, and please tell if it works.

Like that:

if(!Creep.prototype.meleeAttack) {
    _.assign(Creep.prototype,{
        /* ... */,
        getAttackType : getAttackType,
        meleeAttack : Creep.prototype.attack,
        attack : attack_new,
        /* ... */
    }
}