Major Spoiler/Proof of Bane/Neo Fight..Neo`s Eyes
Based upon the available information that we have up to now, this is the only explanation. Everything else would be speculation.
The fight between Neo and Bane takes place abroad Logos and while they are flying to the Machine City.
1) Neo’s fight with Bane aboard the Logos without the benefit of sight, since the prosthetic makeup used to depict Neo’s eye damage severely limited his vision. (From Revolutions Production Notes - Training and Stunts)
2) Though Niobe does not believe in the Oracle’s Prophecy, she offers her ship Logos to Neo when he makes his decision to travel to the Machine City in search of peace.(From Revolutions Production Notes Final Chapter, Official Site)
Now this clearly explains why abroad Logos in one shot we see Neo without the eye bandage and in the other with eyes covered.Also that the fight between Neo and Bane takes place abroad Logos not Hammer.
It`s also safe to disregard any script in which the fight between Neo And Bane occurs anywhere but aboard Logos, like Hammer or.
Regards,
Atreides
P.S. After reading the FDT section for Newbies, I decided to post this on either "Neo’s eyes" or "Blind but not blind" , but since they much strayed from the topic, I posted as a new topic.