You may be thinking of the .rwmacro files? Those contain instructions for Reworder, not JJ2. After you switch tile chunks around in Reworder, they may be in a state that is perfectly interpretable by JJ2 but which JCS will mess up upon saving. The .rwmacro files contain a list of the changes made to the level in Reworder, so that they can be performed again automatically on the level after it has been modified in JCS. They're used for editing, but are totally unnecessary for playing. I would suggest rereading the help file or JCSref article.