Q: If oh i've seen that yes, can we say that "I haven't seen that."?

A: no

Q: If He was up to his hands and knees, and almost managing a walking pace., can we say that "He was in the ocean up to his knees but was still able to walk with ease. "?

A: it is not possible to tell

Q: If 'Is that you?', can we say that "Is it you?"?

A: yes

Q: If Well, perhaps it was, admitted Sir James gravely., can we say that ""Well, I don't think it was" explained Sir James."?

A:
no