Indeed. Sometimes even the most minor changes have to be accounted for in message trees.
For example, if you had a cruiser in mission, the GTC Bob, that would be replaced by the GTC Steve if it were destroyed, it wouldn't make much sense to have all the messages in the mission operate under the assumption the GTC Bob would survive the whole mission. Nor does it make sense for the GTC Steve to have to jump in in the first minute or so. Depending on when the Bob was destroyed, the messages would change. If the Bob is destroyed by SEXP, that's great, but if not, you would have to duplicate all messages that reference one of those names. When that happens in missions I FRED, that usually increases the amount of messages for just those craft by about 50%. The increase expands almost geometrically if you have more than one ship or group that can be destroyed while the mission is still a success.