In addition to what baucoin mentioned above, some of the missions that were used to trigger a cutscene at the end of the previous mission have also been removed and the cutscene moved into the main mission.
For Example, "Secrets of the Ancients" used to be required to trigger a cutscene at the end of "The Power Source".
The cutscene is now a part of "The Power Source", and "Secrets of the Ancients" has been removed accordingly.
To make things even more confusing, "The Power Source" has also been renamed to "Secrets of the Ancients".
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Comments
From the STO Wiki.
Any of those the ones you are talking about?
For Example, "Secrets of the Ancients" used to be required to trigger a cutscene at the end of "The Power Source".
The cutscene is now a part of "The Power Source", and "Secrets of the Ancients" has been removed accordingly.
To make things even more confusing, "The Power Source" has also been renamed to "Secrets of the Ancients".