  The control of any type of quantum hardware invariably necessitates
time-dependent driving. If the basis depends on the control parameter, the
presence of a time-dependent control field yields an extra term in the
Schr\"odinger equation that is often neglected. Here, we examine the effect of
this term in a flux-controlled Majorana junction. We show that a time-varying
flux gives rise to an electromotive force which is amplified when truncating to
the junction's low-energy degrees of freedom. As a result, it compromises the
robustness of the ground-state degeneracy present in the absence of the drive.
The resulting flattening of the energy spectrum can be measured by a strong
suppression of the dc supercurrent.
