When a Flash Pro project is not set up to save automatically, it will prompt you to enable autosave when it has unsaved changes. I usually say yes, because I don't like to lose work. However, Flash considers a file to be "changed" even if you've just popped open a MovieClip to see where that button is so you can duplicate its position elsewhere.
This can make it inconvenient to have a file open to use it for reference as you work in another file, especially if you use version control. Fortunately, I discovered a way to get around this behavior recently.
Simply click the "wrench" icon in the file Properties panel. This will open a dialogue with a check box you can uncheck the Autosave option while you have the file open, using it for reference. If you don't save the file when you close it, your explorations in the file won't be saved and cause your file to show as edited in version control. Since you didn't save the Autosave change either, next time you open it to edit it, it will Autosave as usual.