By "large super" do you mean something your bees are using for storing honey only, or where the brood nest is (which would technically not be a super, but sometimes people call them that). I would not put only 9 frames only down in the brood nest because they will draw it out funny and you might end up injuring good brood (or the queen on a brood frame) trying to pull it up and out. If it truely is a honey super, then sure, only put 9 evenly spaced frames and it will make it easier to cut off the cappings. (Plus 9 frames in a 10 frame super often holds more honey than 10 frames in a 10 frame super). I would not put a medium frame in a deep super. They will fill in the gap and maybe not in a nice way because that violates bee space at the bottom where the frame is "missing".I have questions also. I only have 9 frames in the large super, supposed to have 10. Will that make a difference? I have extra frames for a med super. Could I use one of those even though it is smaller, shorter, not as wide. I'm not sure of the correct terminology!!
Your bees in the pics look happy!!
Sorry about your hive and the flood!! I sure hope someone can answer that for you. You could also look up a beekeeping organization in your area, that could help.