So I guess this is where I become a Cigar Snob, haha. I don't have any flavored cigars but I did put an Acid cigar in an old desktop humidor and all my cigars smelt like that for days. I have a display humidor that has three levels. I have a cigar oasis as my humidification so that takes up about half a tray and I put my churchills on that level. I rotate the top and bottom tray but I keep my Mild to Medium on one tray and my Medium to Full on another. I also remove them all from the cello unless they are an overly odorous cigar.
From what I have heard and found out is that yes, the cigars that 'touch' each other will exchange scents and sometimes even flavors. Many manufactures will keep the same cigars together to let them 'settle' similar to fermenting to blend flavors together and create a more equal flavor after being wrapped - Consistency.
As far as in a humidor I have seen minimal effects but I have still seen some changed. I had a Partagas Black (Darkest cigar I owened at the time) and a Los Blancos Maduro (Also a dark cigar). After 6 months or so I did smoke the Maduro and it did taste a little like the black. Could the wrapper have been dyed? Dunno. Could I be tasting things that my mind made up? Perhaps, but I doubt it. I did take some pictures and posted on twitpic a while ago
http://twitpic.com/gth10
image of normal maduro (for color reference)
http://twitpic.com/h7z6i
6 months sitting in Humidor next to each other.
Enough rambling - I pull them out of cello and organize due to shade of wrapper (i'm going cigar snob, i know. Hate away - haha)