As commenters have mentioned, this is not good English and is quite confusing to read. The sentence as they wrote it doesn't actually mean anything sensical. They could have meant either of these two things:
Regarding your reservation, we have changed your room type from Smoking to Non-smoking.
(Meaning: you did not have a non-smoking room, but now you do.)
Regarding your reservation, we have not changed your room type from Smoking to Non-smoking yet.
(Meaning: we understand you want a non-smoking room, but right now you still have a smoking one; we haven't changed it yet.)
But that doesn't help you, because you still don't know if the room type was changed or not! I assume they did change it, because it would be odd to write back and tell someone you haven't done what they asked yet... And also your request was not for them to change the room status, but to as what the room status was. So a reasonable reply to "Is my room non-smoking?" would be either "Yes, it is." or "No, it wasn't; but we've changed it for you."
To be sure, I'd reply with something like this:
To confirm, my room is now a non-smoking room?
Hopefully the reply should be more easy to understand; a simple "yes" would suffice!