For Save As, Encore copies everything in its folder structure, which includes transcodes of assets while in Encore (using AME or encore). It usually shows its progress, however.
I prefer to "save as" before I start making changes. Encore is just too likely to get confused.
But the way you are doing it, inside Encore is the right way, and it should work.
If you see disk activity, I'd keep waiting.
Force quit can result in problems and you don't have a save as backup yet.