The most common occurence of this being if you attain the +50 flux speed boost, and continue holding down the forward thruster, raising shields or generating any sort of flux actually slows you down. This is a little silly, as if you avoid using the thruster you will retain your momentum.
If you're travelling with +50 speed and try to correct your course, maneuver or slow down deliberately, sure, you stay at the normal cap. I'm definitely not asking for a constant +50 speed. That said, I'm not sure if merely generating flux is enough reason to lose the flux boost. After all, if you have shields up or fire low flux weapons, your dissipation rate keeps your actual flux at 0, so why not allow the flux boost to remain?