We demonstrate time-resolved nonlinear extreme-ultraviolet absorption spectroscopy on multiply charged ions, here applied to the doubly charged neon ion, driven by a phase-locked sequence of two intense free-electron laser pulses. Absorption signatures of resonance lines due to 2$p$--3$d$ bound--bound transitions between the spin-orbit multiplets $^3$P$_{0,1,2}$ and $^3$D$_{1,2,3}$ of the transiently produced doubly charged Ne$^{2+}$ ion are revealed, with time-dependent spectral changes over a time-delay range of $(2.4pm0.3),text{fs}$. Furthermore, we observe 10-meV-scale spectral shifts of these resonances owing to the AC Stark effect. We use a time-dependent quantum model to explain the observations by an enhanced coupling of the ionic quantum states with the partially coherent free-electron-laser radiation when the phase-locked pump and probe pulses precisely overlap in time.
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