The majority of flow shop studies focused so far on permutation schedules, even though non-permutation schedules might offer better results at the expense however of additional computational effort. It is therefore crucial to determine whether the use of non-permutation schedules is justified by the potential improvements that might be obtained. This question becomes particularly interesting in the case of the flow shop problem with missing operations. But, before investigating this question, we must first clarify the definition of a permutation within this context. The objective of this paper consists in bringing out the ambiguity of the definition of a permutation within the flow shop model with missing operations. To overcome this ambiguity, we propose another way of looking at a permutation that includes the classical understanding. Even though, these two definitions may produce different solutions, we present cases where they are equivalent with respect to the makespan criterion.