I am not fully sure if I fully understand your question, but I'll try anyways.
The "Flaming A" was the actual crest on the Atlanta flames jersey. The Flames paid tribute to the previous organization by replacing the Alternate captain A with the Atlanta Flames crest. I have no idea what the rules are regarding this "font swap" for the A on the sweater, but the league hasn't disallowed it or anything. I do believe many fans are aware of the Flaming A and do think it's cool.
The Flaming C is a purely Calgary Flames crest. I don't think you're supposed to replace the captaincy C with an organization's crest. Otherwise, many other organization (ie: Canucks, Montreal etc.) would be able to swap it. However, I don't know the exact rules regarding this. I'm sure it's in probably in the NHL rulebook though.