To ask what may be a stupid question - are you SURE you "cannot save a new version of the project"?
I have found that it takes a VERY long time to do a SAVE AS. Given that I'm usually working on fairly short pieces with mayby 30 minutes of media total, I feel that taking upwards of 15 minutes to save is a long time especially since Encore displays no progress meter or even "working" icon of any kind (not on my Mac; not on my PC). My rule of thumb is that doing a SAVE AS will take about 60% as long as the length of the media in the project, so 60 minutes of media will take 35 to 40 minutes.
It sounds as if you are working on a project with much more than 30 minutes of media. You may simply be running out of patience before the job gets done. If you haven't already, start a SAVE AS and go to lunch. You might be surprised to find it is done when you get back.
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. Recreating a lot of media takes a lot of time. It also takes a lot of HDD space, so be sure you have enough before you start.
JP