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We study the two-body momentum correlation signal in a quasi one dimensional Bose-Einstein condensate in the presence of a sonic horizon. We identify the relevant correlation lines in momentum space and compute the intensity of the corresponding signal. We consider a set of different experimental procedures and identify the specific issues of each measuring process. We show that some inter-channel correlations, in particular the Hawking quantum-partner one, are particularly well adapted for witnessing quantum non-separability, being resilient to the effects of temperature and/or quantum quenches.