Automatic cover detection - the task of finding in an audio dataset all covers of a query track - has long been a challenging theoretical problem in MIR community. It also became a practical need for music composers societies requiring to detect automatically if an audio excerpt embeds musical content belonging to their catalog. In a recent work, we addressed this problem with a convolutional neural network mapping each track's dominant melody to an embedding vector, and trained to minimize cover pairs distance in the embeddings space, while maximizing it for non-covers. We showed in particular that training this model with enough works having five or more covers yields state-of-the-art results. This however does not reflect the realistic use case, where music catalogs typically contain works with zero or at most one or two covers. We thus introduce here a new test set incorporating these constraints, and propose two contributions to improve our model's accuracy under these stricter conditions: we replace dominant melody with multi-pitch representation as input data, and describe a novel prototypical triplet loss designed to improve covers clustering. We show that these changes improve results significantly for two concrete use cases, large dataset lookup and live songs identification.