I have found that it takes a VERY long time to do a SAVE AS.
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As I understand what is going on, Encore is not simply saving a new control track. During a SAVE AS it duplicates ALL the media into a new folder.
Good point re the time it takes. This varies a lot, however, as Encore does not copy media that is outside its project folder, but only transcodes done in Encore (using Encore or AME), which are saved inside these folders. This also means that times can vary with hard drive speeds.
A great feature request is providing a meaningful progress indicator - similar to the build progress with stage and progress within stage.