This paper deals with the measurement of the magnetic flux generated by the armature of electromagnetic rail launchers linked with external pickup loops. In particular we discuss possible methods to experimentally evaluate measurement uncertainty when the magnetic flux is obtained by numerical voltage integration. These methods aim at an approximate identification of the correlation among voltage samples introduced by the analog-to-digital converter, only based on the available measurements without requiring additional tests and instruments. An estimate of this correlation allows to better evaluate the overall measurement uncertainty, thus providing the applicability limits of the proposed inductive technique and contributing to a better understanding of the current and force distribution in the armature.