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In this paper, we deal with the problem of estimating the marking of a labeled Petri net system based on the observation of transitions labels. In particular, we assume that a certain number of transitions are labeled with the empty string , while unique labels taken from a given alphabet are assigned to each of the other transitions. Transitions labeled with the empty string are called silent because their firing cannot be observed. Under some technical assumptions on the structure of the unobservable subnet, we formally prove that the set of markings consistent with the observed word can be represented by a linear system with a fixed structure that does not depend on the length of the observed word.