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How can I resume playback to where the viewer left off if the disc is stopped or removed from the player?
When using DoStudio Indie (BD-J) as you describe this is not possible. (You can use "resume" if the user does not stop the project in play.)
When you press stop or eject the internal java application that manages the Blu-ray is unloaded and thus the resume information is lost as it is not saved. However, if you author using HDMV as with DSA EX, you can script the resume functionality to be saved when a disc is stopped.