Editor wants to change Full Article to Short Communication
Handle this the same way you handle any other dispute: you tell the editor you think the article should be a "Full Article" instead of "Short Communication", giving your reasons. If the editor agrees, problem solved. If editor doesn't agree, it's up to you how much you care how your paper is classified. If you really, really want it to be a full article, you can dig in your heels and withdraw the manuscript if the editor still doesn't agree.

I wouldn't worry about exceeding the word limit for short communications. After all, if the editor didn't ask you to shorten the manuscript, presumably he's going to break the rules in this instance.