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A treaty between the United Federation of Planets and the Serenity Concord, among other things it outlines the rules of how prisoners are dealt with on either side as well as the sharing of intelligence and other security resources.
One of the provisions states that prisoners who are non-military or captured during non-sanctioned operations require that the side who captures the prisoner to be sent all records regarding the prisoner. Failure to do so would constitute a serious violation of the treaty and be seen the same as admitting that the prisoner was there on official business of the government. Such an admission without permission could end in military action and the dissolution of the treaty. Since other aspects of the Temporal Reconciliations rely on this treaty, that is seen as a no-win scenario and would have serious ramifications throughout known space.
Since both sides need each other to manage the time travel threat, there is no situations deedm so serious that the treaty should be put into jeopardy. Both sides subsequently agree to follow best practices in communicating when an operative is working within the bounds of the other.